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- PDB-9ciy: Right-left hybrid parallel G-quadruplex from NSD1 promoter -

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Basic information

Entry
Database: PDB / ID: 9ciy
TitleRight-left hybrid parallel G-quadruplex from NSD1 promoter
ComponentsDNA (25-MER)
KeywordsDNA / G-quadruplex / right-left-handed G-quadruplex / parallel
Function / homology: / COBALT HEXAMMINE(III) / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXing, E.R. / Yatsunyk, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: To be Published
Title: Structure of a left-right-handed G-quadruplex from the promoter of the NSD1 gene
Authors: Xing, E.R. / Yatsunyk, L.A.
History
DepositionJul 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 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 (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,73615
Polymers8,2641
Non-polymers1,47214
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.849, 71.849, 41.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z+1/2
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-104-

K

21A-105-

NCO

31A-105-

NCO

41A-105-

NCO

51A-105-

NCO

61A-105-

NCO

71A-105-

NCO

81A-105-

NCO

91A-203-

HOH

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Components

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DNA chain , 1 types, 1 molecules A

#1: DNA chain DNA (25-MER)


Mass: 8264.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 18 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.32 Å3/Da / Density % sol: 63 % / Description: Large square rods
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M potassium chloride 5 mM Hexammine cobalt chloride 0.05 M MES pH 6.5 25% PEG 4000

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Data collection

DiffractionMean temperature: 196 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 2.39→41.64 Å / Num. obs: 4625 / % possible obs: 99.76 % / Redundancy: 15.1 % / Biso Wilson estimate: 64.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.9
Reflection shellResolution: 2.39→2.49 Å / Redundancy: 14.1 % / Rmerge(I) obs: 2.266 / Num. unique obs: 828 / CC1/2: 0.563 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
Coot0.8.9.2model building
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→32.2 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 219 4.77 %
Rwork0.1968 --
obs0.1984 4588 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→32.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 549 79 4 632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005694
X-RAY DIFFRACTIONf_angle_d0.7621063
X-RAY DIFFRACTIONf_dihedral_angle_d35.808304
X-RAY DIFFRACTIONf_chiral_restr0.041105
X-RAY DIFFRACTIONf_plane_restr0.00526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-3.020.3191060.28382125X-RAY DIFFRACTION100
3.02-32.20.21291130.17952244X-RAY DIFFRACTION99
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)
19.77731.15734.29458.25973.53398.9851-0.5529-0.3253-0.51780.01390.26170.3390.6207-1.35250.38440.7449-0.03380.20420.6159-0.01250.583827.195316.97875.0094
22.1366-1.68290.77381.2477-0.52370.3429-0.5134-0.55-0.33241.13040.6114-1.30721.83190.2998-0.08551.09280.1480.12810.44490.02550.524437.718515.12118.1968
38.2661-5.37145.08067.8811-4.31236.66710.0507-0.291-0.5364-0.38110.49321.42131.3259-1.1089-0.67861.0557-0.15810.14430.6367-0.01680.805328.497912.9442-3.2635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 20 )
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 26 )

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