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- PDB-4xk0: Crystal structure of a tetramolecular RNA G-quadruplex in potassium -

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Basic information

Entry
Database: PDB / ID: 4xk0
TitleCrystal structure of a tetramolecular RNA G-quadruplex in potassium
ComponentsRNA (5'-(*UP*GP*GP*GP*GP*U)-3')
KeywordsRNA / RNA G-quadruplex / tetramolecular G-quadruplex / intermolecular G-quadruplex
Function / homology: / : / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.08 Å
AuthorsChen, M.C. / Murat, P. / Abecassis, K.A. / Ferre-D'Amare, A.R. / Balasubramanian, S.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Insights into the mechanism of a G-quadruplex-unwinding DEAH-box helicase.
Authors: Chen, M.C. / Murat, P. / Abecassis, K. / Ferre-D'Amare, A.R. / Balasubramanian, S.
History
DepositionJan 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Aug 19, 2015Group: Refinement description
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-(*UP*GP*GP*GP*GP*U)-3')
C: RNA (5'-(*UP*GP*GP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,66014
Polymers3,8962
Non-polymers76412
Water1,09961
1
A: RNA (5'-(*UP*GP*GP*GP*GP*U)-3')
C: RNA (5'-(*UP*GP*GP*GP*GP*U)-3')
hetero molecules

A: RNA (5'-(*UP*GP*GP*GP*GP*U)-3')
C: RNA (5'-(*UP*GP*GP*GP*GP*U)-3')
hetero molecules

A: RNA (5'-(*UP*GP*GP*GP*GP*U)-3')
C: RNA (5'-(*UP*GP*GP*GP*GP*U)-3')
hetero molecules

A: RNA (5'-(*UP*GP*GP*GP*GP*U)-3')
C: RNA (5'-(*UP*GP*GP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,64156
Polymers15,5868
Non-polymers3,05548
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area15930 Å2
ΔGint-279 kcal/mol
Surface area1300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.133, 33.133, 54.843
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-101-

K

21A-102-

K

31A-103-

K

41A-104-

K

51A-105-

K

61C-101-

K

71C-102-

K

81C-103-

K

91C-104-

K

101A-209-

HOH

111A-219-

HOH

121A-227-

HOH

131C-226-

HOH

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Components

#1: RNA chain RNA (5'-(*UP*GP*GP*GP*GP*U)-3')


Mass: 1948.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ba
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40 mM potassium cacodylic acid (pH 6.0), 35% 2-methyl-2,4-pentanediol, 5 mM spermine hydrochloride, 80 mM potassium chloride, 0.5 mM DHX36 fragment, 20 mM barium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.8266 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2014
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.07→50 Å / Num. obs: 25610 / % possible obs: 97.4 % / Redundancy: 12.1 % / Biso Wilson estimate: 4.683 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.034 / Rrim(I) all: 0.117 / Χ2: 1.367 / Net I/av σ(I): 19.705 / Net I/σ(I): 31.8 / Num. measured all: 310744
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.07-1.099.40.1876920.9810.0610.1981.87153.5
1.09-1.1111.30.17613200.9840.0540.1851.72599.9
1.11-1.1312.20.16212860.9860.0490.171.663100
1.13-1.1512.10.15313150.9950.0450.161.578100
1.15-1.1812.20.14812990.9910.0440.1541.514100
1.18-1.2112.30.14613160.9910.0430.1521.552100
1.21-1.2412.20.13413260.990.040.1391.414100
1.24-1.2712.30.12913060.9910.0380.1351.343100
1.27-1.3112.30.12413000.9920.0370.1291.338100
1.31-1.3512.40.11712910.9930.0350.1221.273100
1.35-1.412.40.1113340.9940.0320.1151.182100
1.4-1.4512.40.10613070.9960.0310.111.135100
1.45-1.5212.40.113280.9960.0290.1041.166100
1.52-1.612.50.09613020.9960.0280.11.19100
1.6-1.712.40.09413000.9970.0280.0981.07499.8
1.7-1.8312.50.09713230.9970.0290.1011.24799.8
1.83-2.0112.40.09713180.9950.0290.1011.21599.9
2.01-2.3112.30.09813180.9960.0290.1021.23100
2.31-2.9120.10613280.9940.0320.111.35299.8
2.9-5011.30.12813010.9820.0410.1351.68495.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.08→21.54 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.144 --
Rwork0.144 --
obs-25285 99.6 %
Refinement stepCycle: LAST / Resolution: 1.08→21.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 258 12 61 331

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