A Python application to find and classify tetrads and quadruplexes in DNA/RNA 3D structure
Project description
Project description
This is an application to analyze base pairing patterns of DNA/RNA 3D structures to find and classify tetrads and quadruplexes. ElTetrado assigns tetrads to one of the ONZ classes (O, N, Z) alongside with the directionality of the tetrad (+/-) determined by the bonds between bases and their non-canonical interactions. The interactions follow Leontis/Westhof classification (Leontis and Westhof, 2001). Watson-Crick (W) edge of first base in the tetrad structure exposed to the Hoogsteen (H) edge of the next nucleobase from the same tetrad sets the tetrad directionality, clockwise (+) or anticlockwise (-). For more details, please refer to Zok et al. (2020) and Popenda et al. (2020)
Dependencies
The project is written in Python 3.6+ and requires Biopython and NumPy in to run. These can be installed with the following command:
pip install -r requirements.txt
If you have both Python 2 and Python 3 installed, you need to explicitly
call pip3:
pip3 install -r requirements.txt
ElTetrado depends on DSSR (Lu et al., 2015) in terms of detection of
base pairing and stacking. The binary x3dna-dssr can be
downloaded
and put in the same directory as eltetrado which will execute it
during analysis. Alternatively, one can pre-process the 3D data with
x3dna-dssr --json and provide the JSON result as an input to ElTetrado
(see Usage section below).
Visualization is created by R 3.6+ script which uses
R4RNA (Lai et al., 2012) library. The
dependency will be automatically installed if not present.
Usage
ElTetrado is a command line application, which requires to be provided with:
- either
--dssr-jsonand the path to JSON generated withx3dna-dssr --json(fast, but quadruplex parameters likeriseortwistare not calculated) - or
--pdband the path to PDB or PDBx/mmCIF file (slow, because the execution time is a sum of ElTetrado and DSSR times) - or both
--pdband--dssr-json(recommended, all analyses are made and only ElTetrado is executed while DSSR results are read from the file)
By default, ElTetrado outputs textual results on the standard output. A
JSON version of the output can be obtained with --output switch
followed by a path where the file is supposed to be created.
ElTetrado prepares visualization of the whole structure and of each
N4-helices, quadruplexes and tetrads. This can be supplemented with
canonical base pairs visualization when --complete-2d is set. All
color settings are located in the first several lines of the quadraw.R
file, you can easily change them without knowledge of R language. If you
want ElTetrado to not visualize anything, pass --no-image switch to
it.
usage: eltetrado [-h] [--pdb PDB] [--dssr-json DSSR_JSON] [--output OUTPUT]
[--stacking-mismatch STACKING_MISMATCH] [--strict]
[--no-reorder] [--complete-2d] [--no-image] [--version]
optional arguments:
-h, --help show this help message and exit
--pdb PDB path to input PDB or PDBx/mmCIF file
--dssr-json DSSR_JSON
path to input JSON file generated with `x3dna-dssr
--json`
--output OUTPUT (optional) path for output JSON file
--stacking-mismatch STACKING_MISMATCH
a perfect tetrad stacking covers 4 nucleotides; this
option can be used with value 1 or 2 to allow this
number of nucleotides to be non-stacked with otherwise
well aligned tetrad [default=2]
--strict nucleotides in tetrad are found when linked only by
cWH pairing
--no-reorder chains of bi- and tetramolecular quadruplexes are
reordered to be able to have them classified; when
this is set, chains will be processed in original
order and bi-/tetramolecular quadruplexes will not be
classified
--complete-2d when set, the visualization will also show canonical
base pairs to provide context for the quadruplex
--no-image when set, the visualization will not be created at all
--version show program's version number and exit
Chains reorder
ElTetrado keeps a global and unique 5’-3’ index for every nucleotide which is independent from residue numbers. For example, if a structure has chain M with 60 nucleotides and chain N with 15 nucleotides, then ElTetrado will keep index between 0 and 74 which uniquely identifies every nucleotide. Initially, ElTetrado assigns this indices according to the order of chains in the input file. Therefore, if M preceded N then nucleotides in M will be indexed from 0 to 59 and in N from 60 to 74. Otherwise, nucleotides in N will be indexed from 0 to 14 and in M from 15 to 74.
When --no-reorder is present, this initial assignment is used.
Otherwise, ElTetrado exhaustively checks all permutations of chains’
orders. Every permutation check induces recalculation of the global and
unique 5’-3’ index and in effect it changes ONZ classification of
tetrads.
ElTetrado keeps a table of tetrad classification scores according to these rules:
- Type preference:
O>N>Z - Direction preference:
+>-
The table keeps low values for preferred classes i.e. O+ is 0, O- is
1 and so on up to Z- with score 5. For every permutation of chain
orders, ElTetrado computes sum of scores for tetrads classification
induced by 5’-3’ indexing. We select permutation with the minimum value.
Examples
1MY9: Solution structure of a K+ cation stabilized dimeric RNA quadruplex containing two G:G(:A):G:G(:A) hexads, G:G:G:G tetrads and UUUU loops
$ curl ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/my/1my9.cif.gz | gzip -d > 1my9.cif
$ ./eltetrado --pdb 1my9.cif --output 1my9.json
Chain order: A, B
n4-helix with 4 tetrads
Op+ VIII 1a quadruplex with 2 tetrads
B.G16 B.G19 B.G25 B.G28 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.31 ions_channel= ions_outside={}
direction=parallel rise=4.21 twist=33.45
B.G15 B.G18 B.G24 B.G27 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.26 ions_channel= ions_outside={}
Tracts:
B.G25, B.G24
B.G28, B.G27
B.G16, B.G15
B.G19, B.G18
Loops:
propeller- B.A17
propeller- B.U20, B.U21, B.U22, B.U23
propeller- B.A26
Op+ VIII 1a quadruplex with 2 tetrads
A.G1 A.G4 A.G10 A.G13 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.63 ions_channel= ions_outside={}
direction=parallel rise=4.12 twist=28.66
A.G2 A.G5 A.G11 A.G14 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.5 ions_channel= ions_outside={}
Tracts:
A.G10, A.G11
A.G13, A.G14
A.G1, A.G2
A.G4, A.G5
Loops:
propeller- A.A3
propeller- A.U6, A.U7, A.U8, A.U9
propeller- A.A12
GGAGGUUUUGGAGG-GGAGGUUUUGGAGG
([.)]....([.)]-([.)]....([.)]
([.([....)].)]-([.([....)].)]
Click to see the output JSON
{
"metals": "",
"nucleotides": {
"A.G1": {
"index": 1,
"model": 1,
"chain": "A",
"number": 1,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G1",
"short_name": "G",
"chi": -114.063,
"glycosidic_bond": "anti"
},
"A.G2": {
"index": 2,
"model": 1,
"chain": "A",
"number": 2,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G2",
"short_name": "G",
"chi": -136.905,
"glycosidic_bond": "anti"
},
"A.A3": {
"index": 3,
"model": 1,
"chain": "A",
"number": 3,
"icode": " ",
"molecule": "RNA",
"full_name": "A.A3",
"short_name": "A",
"chi": -53.884,
"glycosidic_bond": "syn"
},
"A.G4": {
"index": 4,
"model": 1,
"chain": "A",
"number": 4,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G4",
"short_name": "G",
"chi": 167.763,
"glycosidic_bond": "anti"
},
"A.G5": {
"index": 5,
"model": 1,
"chain": "A",
"number": 5,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G5",
"short_name": "G",
"chi": -98.198,
"glycosidic_bond": "anti"
},
"A.U6": {
"index": 6,
"model": 1,
"chain": "A",
"number": 6,
"icode": " ",
"molecule": "RNA",
"full_name": "A.U6",
"short_name": "U",
"chi": -150.069,
"glycosidic_bond": "anti"
},
"A.U7": {
"index": 7,
"model": 1,
"chain": "A",
"number": 7,
"icode": " ",
"molecule": "RNA",
"full_name": "A.U7",
"short_name": "U",
"chi": -130.523,
"glycosidic_bond": "anti"
},
"A.U8": {
"index": 8,
"model": 1,
"chain": "A",
"number": 8,
"icode": " ",
"molecule": "RNA",
"full_name": "A.U8",
"short_name": "U",
"chi": -158.504,
"glycosidic_bond": "anti"
},
"A.U9": {
"index": 9,
"model": 1,
"chain": "A",
"number": 9,
"icode": " ",
"molecule": "RNA",
"full_name": "A.U9",
"short_name": "U",
"chi": -149.743,
"glycosidic_bond": "anti"
},
"A.G10": {
"index": 10,
"model": 1,
"chain": "A",
"number": 10,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G10",
"short_name": "G",
"chi": -113.245,
"glycosidic_bond": "anti"
},
"A.G11": {
"index": 11,
"model": 1,
"chain": "A",
"number": 11,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G11",
"short_name": "G",
"chi": -138.466,
"glycosidic_bond": "anti"
},
"A.A12": {
"index": 12,
"model": 1,
"chain": "A",
"number": 12,
"icode": " ",
"molecule": "RNA",
"full_name": "A.A12",
"short_name": "A",
"chi": -70.627,
"glycosidic_bond": "syn"
},
"A.G13": {
"index": 13,
"model": 1,
"chain": "A",
"number": 13,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G13",
"short_name": "G",
"chi": 150.585,
"glycosidic_bond": "anti"
},
"A.G14": {
"index": 14,
"model": 1,
"chain": "A",
"number": 14,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G14",
"short_name": "G",
"chi": -158.594,
"glycosidic_bond": "anti"
},
"B.G15": {
"index": 15,
"model": 1,
"chain": "B",
"number": 15,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G15",
"short_name": "G",
"chi": -114.303,
"glycosidic_bond": "anti"
},
"B.G16": {
"index": 16,
"model": 1,
"chain": "B",
"number": 16,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G16",
"short_name": "G",
"chi": -134.388,
"glycosidic_bond": "anti"
},
"B.A17": {
"index": 17,
"model": 1,
"chain": "B",
"number": 17,
"icode": " ",
"molecule": "RNA",
"full_name": "B.A17",
"short_name": "A",
"chi": -52.702,
"glycosidic_bond": "syn"
},
"B.G18": {
"index": 18,
"model": 1,
"chain": "B",
"number": 18,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G18",
"short_name": "G",
"chi": 156.482,
"glycosidic_bond": "anti"
},
"B.G19": {
"index": 19,
"model": 1,
"chain": "B",
"number": 19,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G19",
"short_name": "G",
"chi": -100.234,
"glycosidic_bond": "anti"
},
"B.U20": {
"index": 20,
"model": 1,
"chain": "B",
"number": 20,
"icode": " ",
"molecule": "RNA",
"full_name": "B.U20",
"short_name": "U",
"chi": -146.822,
"glycosidic_bond": "anti"
},
"B.U21": {
"index": 21,
"model": 1,
"chain": "B",
"number": 21,
"icode": " ",
"molecule": "RNA",
"full_name": "B.U21",
"short_name": "U",
"chi": -144.09,
"glycosidic_bond": "anti"
},
"B.U22": {
"index": 22,
"model": 1,
"chain": "B",
"number": 22,
"icode": " ",
"molecule": "RNA",
"full_name": "B.U22",
"short_name": "U",
"chi": -160.945,
"glycosidic_bond": "anti"
},
"B.U23": {
"index": 23,
"model": 1,
"chain": "B",
"number": 23,
"icode": " ",
"molecule": "RNA",
"full_name": "B.U23",
"short_name": "U",
"chi": -144.171,
"glycosidic_bond": "anti"
},
"B.G24": {
"index": 24,
"model": 1,
"chain": "B",
"number": 24,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G24",
"short_name": "G",
"chi": -121.507,
"glycosidic_bond": "anti"
},
"B.G25": {
"index": 25,
"model": 1,
"chain": "B",
"number": 25,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G25",
"short_name": "G",
"chi": -132.739,
"glycosidic_bond": "anti"
},
"B.A26": {
"index": 26,
"model": 1,
"chain": "B",
"number": 26,
"icode": " ",
"molecule": "RNA",
"full_name": "B.A26",
"short_name": "A",
"chi": -72.432,
"glycosidic_bond": "syn"
},
"B.G27": {
"index": 27,
"model": 1,
"chain": "B",
"number": 27,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G27",
"short_name": "G",
"chi": -178.717,
"glycosidic_bond": "anti"
},
"B.G28": {
"index": 28,
"model": 1,
"chain": "B",
"number": 28,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G28",
"short_name": "G",
"chi": -130.902,
"glycosidic_bond": "anti"
}
},
"base_pairs": [
{
"nt1": "A.G1",
"nt2": "A.A3",
"stericity": "trans",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "A.A3",
"nt2": "A.G1",
"stericity": "trans",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "A.G1",
"nt2": "A.G4",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.G4",
"nt2": "A.G1",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G1",
"nt2": "A.G13",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G13",
"nt2": "A.G1",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.G2",
"nt2": "A.G5",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.G5",
"nt2": "A.G2",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G2",
"nt2": "A.G11",
"stericity": "trans",
"edge5": "Watson-Crick",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G11",
"nt2": "A.G2",
"stericity": "trans",
"edge5": "Watson-Crick",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G2",
"nt2": "A.G14",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G14",
"nt2": "A.G2",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.G4",
"nt2": "A.G10",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.G10",
"nt2": "A.G4",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G4",
"nt2": "B.A17",
"stericity": "trans",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "B.A17",
"nt2": "A.G4",
"stericity": "trans",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "A.G5",
"nt2": "A.G11",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.G11",
"nt2": "A.G5",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G10",
"nt2": "A.A12",
"stericity": "trans",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "A.A12",
"nt2": "A.G10",
"stericity": "trans",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "A.G10",
"nt2": "A.G13",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.G13",
"nt2": "A.G10",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G11",
"nt2": "A.G14",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.G14",
"nt2": "A.G11",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G13",
"nt2": "B.G27",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "B.G27",
"nt2": "A.G13",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Hoogsteen"
},
{
"nt1": "B.G15",
"nt2": "B.A17",
"stericity": "trans",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "B.A17",
"nt2": "B.G15",
"stericity": "trans",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "B.G15",
"nt2": "B.G18",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.G18",
"nt2": "B.G15",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.G15",
"nt2": "B.G27",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.G27",
"nt2": "B.G15",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.G16",
"nt2": "B.G19",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.G19",
"nt2": "B.G16",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.G16",
"nt2": "B.G28",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.G28",
"nt2": "B.G16",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.G18",
"nt2": "B.G24",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.G24",
"nt2": "B.G18",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.G19",
"nt2": "B.G25",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.G25",
"nt2": "B.G19",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.G24",
"nt2": "B.A26",
"stericity": "trans",
"edge5": "Sugar",
"edge3": "Hoogsteen"
},
{
"nt1": "B.A26",
"nt2": "B.G24",
"stericity": "trans",
"edge5": "Hoogsteen",
"edge3": "Sugar"
},
{
"nt1": "B.G24",
"nt2": "B.G27",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.G27",
"nt2": "B.G24",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "B.G25",
"nt2": "B.G28",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "B.G28",
"nt2": "B.G25",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
}
],
"helices": [
{
"quadruplexes": [
{
"tetrads": {
"B.G16-B.G19-B.G25-B.G28": {
"nt1": "B.G16",
"nt2": "B.G19",
"nt3": "B.G25",
"nt4": "B.G28",
"onz": "O+",
"gba_classification": "VIIIa",
"planarity_deviation": 0.31002684978384765,
"ions_channel": [],
"ions_outside": {}
},
"B.G15-B.G18-B.G24-B.G27": {
"nt1": "B.G15",
"nt2": "B.G18",
"nt3": "B.G24",
"nt4": "B.G27",
"onz": "O+",
"gba_classification": "VIIIa",
"planarity_deviation": 0.2616979115189099,
"ions_channel": [],
"ions_outside": {}
}
},
"onzm": "Op+",
"loop_classification": "1a",
"gba_classification": "VIII",
"tracts": [
[
"B.G25",
"B.G24"
],
[
"B.G28",
"B.G27"
],
[
"B.G16",
"B.G15"
],
[
"B.G19",
"B.G18"
]
],
"loops": [
{
"loop_type": "propeller-",
"nucleotides": [
"B.A17"
]
},
{
"loop_type": "propeller-",
"nucleotides": [
"B.U20",
"B.U21",
"B.U22",
"B.U23"
]
},
{
"loop_type": "propeller-",
"nucleotides": [
"B.A26"
]
}
]
},
{
"tetrads": {
"A.G1-A.G4-A.G10-A.G13": {
"nt1": "A.G1",
"nt2": "A.G4",
"nt3": "A.G10",
"nt4": "A.G13",
"onz": "O+",
"gba_classification": "VIIIa",
"planarity_deviation": 0.6331163330540677,
"ions_channel": [],
"ions_outside": {}
},
"A.G2-A.G5-A.G11-A.G14": {
"nt1": "A.G2",
"nt2": "A.G5",
"nt3": "A.G11",
"nt4": "A.G14",
"onz": "O+",
"gba_classification": "VIIIa",
"planarity_deviation": 0.49745503003636027,
"ions_channel": [],
"ions_outside": {}
}
},
"onzm": "Op+",
"loop_classification": "1a",
"gba_classification": "VIII",
"tracts": [
[
"A.G10",
"A.G11"
],
[
"A.G13",
"A.G14"
],
[
"A.G1",
"A.G2"
],
[
"A.G4",
"A.G5"
]
],
"loops": [
{
"loop_type": "propeller-",
"nucleotides": [
"A.A3"
]
},
{
"loop_type": "propeller-",
"nucleotides": [
"A.U6",
"A.U7",
"A.U8",
"A.U9"
]
},
{
"loop_type": "propeller-",
"nucleotides": [
"A.A12"
]
}
]
}
],
"tetrad_pairs": [
{
"tetrad1": "B.G16-B.G19-B.G25-B.G28",
"tetrad2": "B.G15-B.G18-B.G24-B.G27",
"direction": "parallel",
"rise": 4.211160689840694,
"twist": 33.44705121023191
},
{
"tetrad1": "B.G15-B.G18-B.G24-B.G27",
"tetrad2": "A.G1-A.G4-A.G10-A.G13",
"direction": "parallel",
"rise": 3.184510351147094,
"twist": 2.4776498925690027
},
{
"tetrad1": "A.G1-A.G4-A.G10-A.G13",
"tetrad2": "A.G2-A.G5-A.G11-A.G14",
"direction": "parallel",
"rise": 4.121721871766505,
"twist": 28.658873381786407
}
]
}
]
}
4RJ1: Structural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions
$ curl https://www.ebi.ac.uk/pdbe/static/entry/download/4rj1-assembly-1.cif.gz | gzip -d > 4rj1-1.cif
$ ./eltetrado --pdb 4rj1-1.cif --output 4rj1-1.json
Chain order: A, AB, AA, AC, B, BC, BA, BB
n4-helix with 10 tetrads
Op* VIII n/a quadruplex with 5 tetrads
B.U2006 BB.U2006 BA.U2006 BC.U2006 cWH-cWH-cWH-cWH O- VIIIa planarity=1.58 ions_channel=NA,NA ions_outside={}
direction=parallel rise=7.14 twist=43.41
B.G2005 BC.G2005 BA.G2005 BB.G2005 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.78 ions_channel= ions_outside={}
direction=parallel rise=3.27 twist=25.15
B.G2004 BC.G2004 BA.G2004 BB.G2004 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.23 ions_channel=SR ions_outside={}
direction=parallel rise=3.32 twist=35.04
B.G2003 BC.G2003 BA.G2003 BB.G2003 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.58 ions_channel=SR ions_outside={}
direction=parallel rise=3.37 twist=27.41
B.G2002 BC.G2002 BA.G2002 BB.G2002 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.67 ions_channel= ions_outside={}
Tracts:
BA.U2006, BA.G2005, BA.G2004, BA.G2003, BA.G2002
BC.U2006, BC.G2005, BC.G2004, BC.G2003, BC.G2002
B.U2006, B.G2005, B.G2004, B.G2003, B.G2002
BB.U2006, BB.G2005, BB.G2004, BB.G2003, BB.G2002
Op* VIII n/a quadruplex with 5 tetrads
A.G1002 AB.G1002 AA.G1002 AC.G1002 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.54 ions_channel= ions_outside={}
direction=parallel rise=3.29 twist=27.12
A.G1003 AB.G1003 AA.G1003 AC.G1003 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.56 ions_channel=SR ions_outside={}
direction=parallel rise=3.34 twist=35.81
A.G1004 AB.G1004 AA.G1004 AC.G1004 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.41 ions_channel= ions_outside={}
direction=parallel rise=3.31 twist=25.9
A.G1005 AB.G1005 AA.G1005 AC.G1005 cWH-cWH-cWH-cWH O+ VIIIa planarity=0.8 ions_channel=SR ions_outside={}
direction=parallel rise=3.37 twist=39.96
A.U1006 AC.U1006 AA.U1006 AB.U1006 cWH-cWH-cWH-cWH O- VIIIa planarity=1.06 ions_channel= ions_outside={A.U1006: 'SR', AA.U1006: 'SR', AB.U1006: 'SR', AC.U1006: 'SR'}
Tracts:
AA.G1002, AA.G1003, AA.G1004, AA.G1005, AA.U1006
AC.G1002, AC.G1003, AC.G1004, AC.G1005, AC.U1006
A.G1002, A.G1003, A.G1004, A.G1005, A.U1006
AB.G1002, AB.G1003, AB.G1004, AB.G1005, AB.U1006
UGGGGU-UGGGGU-UGGGGU-UGGGGU-UGGGGU-UGGGGU-UGGGGU-UGGGGU
.([{<A-.)]}>A-.([{<a-.)]}>a-.([{<A-.)]}>A-.([{<a-.)]}>a
.([{<A-.([{<a-.)]}>A-.)]}>a-.([{<A-.([{<a-.)]}>A-.)]}>a
Click to see the output JSON
{
"metals": "Ca=12,Na=2,Sr=8",
"nucleotides": {
"A.U1001": {
"index": 1,
"model": 1,
"chain": "A",
"number": 1001,
"icode": " ",
"molecule": "RNA",
"full_name": "A.U1001",
"short_name": "U",
"chi": -141.927,
"glycosidic_bond": "anti"
},
"A.G1002": {
"index": 2,
"model": 1,
"chain": "A",
"number": 1002,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G1002",
"short_name": "G",
"chi": -165.93,
"glycosidic_bond": "anti"
},
"A.G1003": {
"index": 3,
"model": 1,
"chain": "A",
"number": 1003,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G1003",
"short_name": "G",
"chi": -121.565,
"glycosidic_bond": "anti"
},
"A.G1004": {
"index": 4,
"model": 1,
"chain": "A",
"number": 1004,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G1004",
"short_name": "G",
"chi": -156.01,
"glycosidic_bond": "anti"
},
"A.G1005": {
"index": 5,
"model": 1,
"chain": "A",
"number": 1005,
"icode": " ",
"molecule": "RNA",
"full_name": "A.G1005",
"short_name": "G",
"chi": -148.101,
"glycosidic_bond": "anti"
},
"A.U1006": {
"index": 6,
"model": 1,
"chain": "A",
"number": 1006,
"icode": " ",
"molecule": "RNA",
"full_name": "A.U1006",
"short_name": "U",
"chi": -137.28,
"glycosidic_bond": "anti"
},
"AA.U1001": {
"index": 13,
"model": 1,
"chain": "AA",
"number": 1001,
"icode": " ",
"molecule": "RNA",
"full_name": "AA.U1001",
"short_name": "U",
"chi": -141.927,
"glycosidic_bond": "anti"
},
"AA.G1002": {
"index": 14,
"model": 1,
"chain": "AA",
"number": 1002,
"icode": " ",
"molecule": "RNA",
"full_name": "AA.G1002",
"short_name": "G",
"chi": -165.93,
"glycosidic_bond": "anti"
},
"AA.G1003": {
"index": 15,
"model": 1,
"chain": "AA",
"number": 1003,
"icode": " ",
"molecule": "RNA",
"full_name": "AA.G1003",
"short_name": "G",
"chi": -121.565,
"glycosidic_bond": "anti"
},
"AA.G1004": {
"index": 16,
"model": 1,
"chain": "AA",
"number": 1004,
"icode": " ",
"molecule": "RNA",
"full_name": "AA.G1004",
"short_name": "G",
"chi": -156.01,
"glycosidic_bond": "anti"
},
"AA.G1005": {
"index": 17,
"model": 1,
"chain": "AA",
"number": 1005,
"icode": " ",
"molecule": "RNA",
"full_name": "AA.G1005",
"short_name": "G",
"chi": -148.101,
"glycosidic_bond": "anti"
},
"AA.U1006": {
"index": 18,
"model": 1,
"chain": "AA",
"number": 1006,
"icode": " ",
"molecule": "RNA",
"full_name": "AA.U1006",
"short_name": "U",
"chi": -137.28,
"glycosidic_bond": "anti"
},
"AB.U1001": {
"index": 7,
"model": 1,
"chain": "AB",
"number": 1001,
"icode": " ",
"molecule": "RNA",
"full_name": "AB.U1001",
"short_name": "U",
"chi": -141.927,
"glycosidic_bond": "anti"
},
"AB.G1002": {
"index": 8,
"model": 1,
"chain": "AB",
"number": 1002,
"icode": " ",
"molecule": "RNA",
"full_name": "AB.G1002",
"short_name": "G",
"chi": -165.93,
"glycosidic_bond": "anti"
},
"AB.G1003": {
"index": 9,
"model": 1,
"chain": "AB",
"number": 1003,
"icode": " ",
"molecule": "RNA",
"full_name": "AB.G1003",
"short_name": "G",
"chi": -121.565,
"glycosidic_bond": "anti"
},
"AB.G1004": {
"index": 10,
"model": 1,
"chain": "AB",
"number": 1004,
"icode": " ",
"molecule": "RNA",
"full_name": "AB.G1004",
"short_name": "G",
"chi": -156.01,
"glycosidic_bond": "anti"
},
"AB.G1005": {
"index": 11,
"model": 1,
"chain": "AB",
"number": 1005,
"icode": " ",
"molecule": "RNA",
"full_name": "AB.G1005",
"short_name": "G",
"chi": -148.101,
"glycosidic_bond": "anti"
},
"AB.U1006": {
"index": 12,
"model": 1,
"chain": "AB",
"number": 1006,
"icode": " ",
"molecule": "RNA",
"full_name": "AB.U1006",
"short_name": "U",
"chi": -137.28,
"glycosidic_bond": "anti"
},
"AC.U1001": {
"index": 19,
"model": 1,
"chain": "AC",
"number": 1001,
"icode": " ",
"molecule": "RNA",
"full_name": "AC.U1001",
"short_name": "U",
"chi": -141.927,
"glycosidic_bond": "anti"
},
"AC.G1002": {
"index": 20,
"model": 1,
"chain": "AC",
"number": 1002,
"icode": " ",
"molecule": "RNA",
"full_name": "AC.G1002",
"short_name": "G",
"chi": -165.93,
"glycosidic_bond": "anti"
},
"AC.G1003": {
"index": 21,
"model": 1,
"chain": "AC",
"number": 1003,
"icode": " ",
"molecule": "RNA",
"full_name": "AC.G1003",
"short_name": "G",
"chi": -121.565,
"glycosidic_bond": "anti"
},
"AC.G1004": {
"index": 22,
"model": 1,
"chain": "AC",
"number": 1004,
"icode": " ",
"molecule": "RNA",
"full_name": "AC.G1004",
"short_name": "G",
"chi": -156.01,
"glycosidic_bond": "anti"
},
"AC.G1005": {
"index": 23,
"model": 1,
"chain": "AC",
"number": 1005,
"icode": " ",
"molecule": "RNA",
"full_name": "AC.G1005",
"short_name": "G",
"chi": -148.101,
"glycosidic_bond": "anti"
},
"AC.U1006": {
"index": 24,
"model": 1,
"chain": "AC",
"number": 1006,
"icode": " ",
"molecule": "RNA",
"full_name": "AC.U1006",
"short_name": "U",
"chi": -137.28,
"glycosidic_bond": "anti"
},
"B.U2001": {
"index": 25,
"model": 1,
"chain": "B",
"number": 2001,
"icode": " ",
"molecule": "RNA",
"full_name": "B.U2001",
"short_name": "U",
"chi": -146.462,
"glycosidic_bond": "anti"
},
"B.G2002": {
"index": 26,
"model": 1,
"chain": "B",
"number": 2002,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G2002",
"short_name": "G",
"chi": -170.797,
"glycosidic_bond": "anti"
},
"B.G2003": {
"index": 27,
"model": 1,
"chain": "B",
"number": 2003,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G2003",
"short_name": "G",
"chi": -117.687,
"glycosidic_bond": "anti"
},
"B.G2004": {
"index": 28,
"model": 1,
"chain": "B",
"number": 2004,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G2004",
"short_name": "G",
"chi": -153.886,
"glycosidic_bond": "anti"
},
"B.G2005": {
"index": 29,
"model": 1,
"chain": "B",
"number": 2005,
"icode": " ",
"molecule": "RNA",
"full_name": "B.G2005",
"short_name": "G",
"chi": -148.852,
"glycosidic_bond": "anti"
},
"B.U2006": {
"index": 30,
"model": 1,
"chain": "B",
"number": 2006,
"icode": " ",
"molecule": "RNA",
"full_name": "B.U2006",
"short_name": "U",
"chi": -159.437,
"glycosidic_bond": "anti"
},
"BA.U2001": {
"index": 37,
"model": 1,
"chain": "BA",
"number": 2001,
"icode": " ",
"molecule": "RNA",
"full_name": "BA.U2001",
"short_name": "U",
"chi": -146.462,
"glycosidic_bond": "anti"
},
"BA.G2002": {
"index": 38,
"model": 1,
"chain": "BA",
"number": 2002,
"icode": " ",
"molecule": "RNA",
"full_name": "BA.G2002",
"short_name": "G",
"chi": -170.797,
"glycosidic_bond": "anti"
},
"BA.G2003": {
"index": 39,
"model": 1,
"chain": "BA",
"number": 2003,
"icode": " ",
"molecule": "RNA",
"full_name": "BA.G2003",
"short_name": "G",
"chi": -117.687,
"glycosidic_bond": "anti"
},
"BA.G2004": {
"index": 40,
"model": 1,
"chain": "BA",
"number": 2004,
"icode": " ",
"molecule": "RNA",
"full_name": "BA.G2004",
"short_name": "G",
"chi": -153.886,
"glycosidic_bond": "anti"
},
"BA.G2005": {
"index": 41,
"model": 1,
"chain": "BA",
"number": 2005,
"icode": " ",
"molecule": "RNA",
"full_name": "BA.G2005",
"short_name": "G",
"chi": -148.852,
"glycosidic_bond": "anti"
},
"BA.U2006": {
"index": 42,
"model": 1,
"chain": "BA",
"number": 2006,
"icode": " ",
"molecule": "RNA",
"full_name": "BA.U2006",
"short_name": "U",
"chi": -159.437,
"glycosidic_bond": "anti"
},
"BB.U2001": {
"index": 43,
"model": 1,
"chain": "BB",
"number": 2001,
"icode": " ",
"molecule": "RNA",
"full_name": "BB.U2001",
"short_name": "U",
"chi": -146.462,
"glycosidic_bond": "anti"
},
"BB.G2002": {
"index": 44,
"model": 1,
"chain": "BB",
"number": 2002,
"icode": " ",
"molecule": "RNA",
"full_name": "BB.G2002",
"short_name": "G",
"chi": -170.797,
"glycosidic_bond": "anti"
},
"BB.G2003": {
"index": 45,
"model": 1,
"chain": "BB",
"number": 2003,
"icode": " ",
"molecule": "RNA",
"full_name": "BB.G2003",
"short_name": "G",
"chi": -117.687,
"glycosidic_bond": "anti"
},
"BB.G2004": {
"index": 46,
"model": 1,
"chain": "BB",
"number": 2004,
"icode": " ",
"molecule": "RNA",
"full_name": "BB.G2004",
"short_name": "G",
"chi": -153.886,
"glycosidic_bond": "anti"
},
"BB.G2005": {
"index": 47,
"model": 1,
"chain": "BB",
"number": 2005,
"icode": " ",
"molecule": "RNA",
"full_name": "BB.G2005",
"short_name": "G",
"chi": -148.852,
"glycosidic_bond": "anti"
},
"BB.U2006": {
"index": 48,
"model": 1,
"chain": "BB",
"number": 2006,
"icode": " ",
"molecule": "RNA",
"full_name": "BB.U2006",
"short_name": "U",
"chi": -159.437,
"glycosidic_bond": "anti"
},
"BC.U2001": {
"index": 31,
"model": 1,
"chain": "BC",
"number": 2001,
"icode": " ",
"molecule": "RNA",
"full_name": "BC.U2001",
"short_name": "U",
"chi": -146.462,
"glycosidic_bond": "anti"
},
"BC.G2002": {
"index": 32,
"model": 1,
"chain": "BC",
"number": 2002,
"icode": " ",
"molecule": "RNA",
"full_name": "BC.G2002",
"short_name": "G",
"chi": -170.797,
"glycosidic_bond": "anti"
},
"BC.G2003": {
"index": 33,
"model": 1,
"chain": "BC",
"number": 2003,
"icode": " ",
"molecule": "RNA",
"full_name": "BC.G2003",
"short_name": "G",
"chi": -117.687,
"glycosidic_bond": "anti"
},
"BC.G2004": {
"index": 34,
"model": 1,
"chain": "BC",
"number": 2004,
"icode": " ",
"molecule": "RNA",
"full_name": "BC.G2004",
"short_name": "G",
"chi": -153.886,
"glycosidic_bond": "anti"
},
"BC.G2005": {
"index": 35,
"model": 1,
"chain": "BC",
"number": 2005,
"icode": " ",
"molecule": "RNA",
"full_name": "BC.G2005",
"short_name": "G",
"chi": -148.852,
"glycosidic_bond": "anti"
},
"BC.U2006": {
"index": 36,
"model": 1,
"chain": "BC",
"number": 2006,
"icode": " ",
"molecule": "RNA",
"full_name": "BC.U2006",
"short_name": "U",
"chi": -159.437,
"glycosidic_bond": "anti"
}
},
"base_pairs": [
{
"nt1": "A.U1001",
"nt2": "B.G2003",
"stericity": "cis",
"edge5": "Sugar",
"edge3": "Sugar"
},
{
"nt1": "B.G2003",
"nt2": "A.U1001",
"stericity": "cis",
"edge5": "Sugar",
"edge3": "Sugar"
},
{
"nt1": "A.G1002",
"nt2": "AB.G1002",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "AB.G1002",
"nt2": "A.G1002",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G1002",
"nt2": "AC.G1002",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "AC.G1002",
"nt2": "A.G1002",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.G1003",
"nt2": "AB.G1003",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "AB.G1003",
"nt2": "A.G1003",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "A.G1003",
"nt2": "AC.G1003",
"stericity": "cis",
"edge5": "Hoogsteen",
"edge3": "Watson-Crick"
},
{
"nt1": "AC.G1003",
"nt2": "A.G1003",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "A.G1003",
"nt2": "B.U2001",
"stericity": "cis",
"edge5": "Sugar",
"edge3": "Sugar"
},
{
"nt1": "B.U2001",
"nt2": "A.G1003",
"stericity": "cis",
"edge5": "Sugar",
"edge3": "Sugar"
},
{
"nt1": "A.G1004",
"nt2": "AB.G1004",
"stericity": "cis",
"edge5": "Watson-Crick",
"edge3": "Hoogsteen"
},
{
"nt1": "AB.G1004",
"nt2": "A.G1004",
"stericity": "cis",
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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]
}
]
}
Funding
This research was supported by the National Science Centre, Poland [2016/23/B/ST6/03931, 2019/35/B/ST6/03074] and Mloda Kadra project [09/91/SBAD/0684] from Poznan University of Technology, and carried out in the European Centre for Bioinformatics and Genomics (Poland). The authors also acknowledge partial support by the statutory funds of Poznan University of Technology, Polish Ministry of Science and Higher Education, and the Institute of Bioorganic Chemistry, PAS within intramural financing program.
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