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- PDB-9uk6: Dimeric parallel G-quadruplex formed by d(G4C2)4 -

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Basic information

Entry
Database: PDB / ID: 9uk6
TitleDimeric parallel 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*C)-3')
KeywordsDNA / G-quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6925
Polymers7,5361
Non-polymers1564
Water41423
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*C)-3')
hetero molecules

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*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,38410
Polymers15,0722
Non-polymers3138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Unit cell
Length a, b, c (Å)64.036, 64.036, 33.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-104-

K

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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*C)-3')


Mass: 7535.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M Potassium chloride, 0.05 M Sodium cacodylate trihydrate at pH 6.0, 16% w/v Polyethylene glycol 1,000, and 0.0005 M Spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.91776 Å
DetectorType: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: May 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91776 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 5104 / % possible obs: 99.8 % / Redundancy: 12.76 % / CC1/2: 0.999 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.154 / Net I/σ(I): 12.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.94-2.0613.522.4171.148090.5072.51199.4
2.06-2.213.41.0992.617780.8571.143100
2.2-2.3712.950.6923.97050.9490.721100
2.37-2.612.650.3477.316550.9860.362100
2.6-2.9112.990.23110.926060.9940.24100
2.91-3.3512.160.0819.7353610.083100
3.35-4.112.830.07228.794530.9990.075100
4.1-5.7811.60.0637.13510.9980.063100
5.78-509.890.05439.521110.05798.6

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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: 7ECG

7ecg


Resolution: 1.94→29.56 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.191 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.193 / 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
Rfree0.2838 512 10 %RANDOM
Rwork0.24222 ---
obs0.24635 4591 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.412 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2---1.8 Å20 Å2
3---3.59 Å2
Refinement stepCycle: LAST / Resolution: 1.94→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 501 4 23 528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.009564
X-RAY DIFFRACTIONr_bond_other_d0.0010.017264
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.325872
X-RAY DIFFRACTIONr_angle_other_deg0.4391.577624
X-RAY DIFFRACTIONr_chiral_restr0.0440.295
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0296
X-RAY DIFFRACTIONr_scbond_it4.4712.929564
X-RAY DIFFRACTIONr_scbond_other4.4672.93565
X-RAY DIFFRACTIONr_scangle_other6.9065.285873
X-RAY DIFFRACTIONr_long_range_B_refined6.73843.212889
X-RAY DIFFRACTIONr_long_range_B_other6.7443.222886
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.632 47 -
Rwork0.495 315 -
obs--98.64 %
Refinement TLS params.Method: refined / Origin x: 7.45 Å / Origin y: -2.677 Å / Origin z: -13.78 Å
111213212223313233
T0.0278 Å2-0.0139 Å20.0131 Å2-0.1433 Å2-0.0083 Å2--0.0703 Å2
L6.3759 °2-2.0878 °20.0592 °2-7.2292 °2-1.1619 °2--4.4114 °2
S-0.0436 Å °0.2672 Å °0.1579 Å °-0.1154 Å °-0.0019 Å °-0.5934 Å °-0.1069 Å °0.0867 Å °0.0455 Å °

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