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- PDB-9uk8: Monomeric antiparallel G-quadruplex formed by d(G4C2)4 -

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Basic information

Entry
Database: PDB / ID: 9uk8
TitleMonomeric antiparallel G-quadruplex formed by d(G4C2)4
ComponentsDNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP)-3')
KeywordsDNA / G-quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGeng, Y. / Cai, Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32301023 China
National Science Foundation (NSF, China)32471312 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Crystal structures of distinct parallel and antiparallel DNA G-quadruplexes reveal structural polymorphism in C9orf72 G4C2 repeats.
Authors: Geng, Y. / Liu, C. / Miao, H. / Suen, M.C. / Xie, Y. / Zhang, B. / Han, W. / Wu, C. / Ren, H. / Chen, X. / Tai, H.C. / Wang, Z. / Zhu, G. / Cai, Q.
History
DepositionApr 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP)-3')
B: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP)-3')
C: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP)-3')
D: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,76920
Polymers30,1434
Non-polymers62616
Water1086
1
A: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6925
Polymers7,5361
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6925
Polymers7,5361
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6925
Polymers7,5361
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6925
Polymers7,5361
Non-polymers1564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.288, 87.147, 98.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain
DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP)-3')


Mass: 7535.790 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05 M KCl, 0.05 M BIS-TRIS at pH 7.0, 33% w/v PEG 3350 and 0.005 M spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.919764 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919764 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 7881 / % possible obs: 99.8 % / Redundancy: 9.8 % / CC1/2: 1 / Rmerge(I) obs: 0.16 / Rrim(I) all: 0.169 / Net I/σ(I): 12.12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.868.881.5771.7412400.3351.67699.2
2.86-3.0610.41.2012.4511600.771.264100
3.06-3.310.350.4325.4410870.9860.455100
3.3-3.629.890.210.2310080.9970.211100
3.62-4.0410.260.16612.79290.9980.175100
4.04-4.669.860.1218.228310.9980.127100
4.66-5.699.950.08725.017000.9980.092100
5.69-7.989.290.05829.9758010.06299.8
7.98-508.220.0353634610.03898.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2N2D

2n2d


Resolution: 2.7→43.61 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / SU B: 35.66 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 775 9.8 %RANDOM
Rwork0.23336 ---
obs0.23518 7100 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.503 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0 Å20 Å2
2--2.15 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1894 16 6 1916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0092132
X-RAY DIFFRACTIONr_bond_other_d0.0020.017990
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.3193295
X-RAY DIFFRACTIONr_angle_other_deg0.5381.582340
X-RAY DIFFRACTIONr_chiral_restr0.0660.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021182
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
X-RAY DIFFRACTIONr_scbond_it1.9244.112132
X-RAY DIFFRACTIONr_scbond_other1.9244.1122133
X-RAY DIFFRACTIONr_scangle_other3.0637.3953296
X-RAY DIFFRACTIONr_long_range_B_refined7.79184.0712128
X-RAY DIFFRACTIONr_long_range_B_other7.78684.112117
LS refinement shellResolution: 2.7→2.769 Å
RfactorNum. reflection% reflection
Rfree0.415 58 -
Rwork0.424 495 -
obs--98.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.9009-1.91420.55653.3311-0.54755.1528-0.09020.8378-0.1288-0.6380.2701-0.03080.2407-0.0439-0.180.2523-0.0920.02780.2131-0.0260.02575.834-0.53521.995
26.82592.32280.34654.198-0.35792.85370.0573-0.57860.33640.45560.06010.2204-0.0136-0.0694-0.11750.21620.0832-0.00210.0902-0.02720.0272-5.5240.572.32
39.5461-0.7234-0.64912.9798-0.01396.33280.1206-0.12811.5597-0.1202-0.07310.3263-1.1212-0.3289-0.04760.33480.0545-0.00290.07-0.03440.3236-0.683-27.90910.804
49.7426-0.913-0.16213.8812-0.50526.20350.00380.2504-1.5721-0.194-0.0662-0.33361.24440.21250.06240.3852-0.00070.06160.1375-0.07360.3339-14.713-17.26135.737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2B1 - 23
3X-RAY DIFFRACTION3C1 - 24
4X-RAY DIFFRACTION4D1 - 24

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