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- PDB-7ysf: Crystal structure of ZNF524 ZF1-4 in complex with telomeric DNA -

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Basic information

Entry
Database: PDB / ID: 7ysf
TitleCrystal structure of ZNF524 ZF1-4 in complex with telomeric DNA
Components
  • DNA (5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*C)-3')
  • Zinc finger protein 524
KeywordsTRANSFERASE/DNA / C2H2 zinc finger / DNA BINDING PROTEIN / TRANSFERASE-DNA complex
Function / homology
Function and homology information


sequence-specific double-stranded DNA binding / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus / metal ion binding
Similarity search - Function
C2H2-type zinc finger / C2H2-type zinc finger / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
D-MALATE / DNA / DNA (> 10) / Zinc finger protein 524
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsLi, F.D. / Xu, Z.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: ZNF524 directly interacts with telomeric DNA and supports telomere integrity.
Authors: Braun, H. / Xu, Z. / Chang, F. / Viceconte, N. / Rane, G. / Levin, M. / Lototska, L. / Roth, F. / Hillairet, A. / Fradera-Sola, A. / Khanchandani, V. / Sin, Z.W. / Yong, W.K. / Dreesen, O. / ...Authors: Braun, H. / Xu, Z. / Chang, F. / Viceconte, N. / Rane, G. / Levin, M. / Lototska, L. / Roth, F. / Hillairet, A. / Fradera-Sola, A. / Khanchandani, V. / Sin, Z.W. / Yong, W.K. / Dreesen, O. / Yang, Y. / Shi, Y. / Li, F. / Butter, F. / Kappei, D.
History
DepositionAug 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein 524
B: DNA (5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*G)-3')
C: DNA (5'-D(*TP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1648
Polymers24,7683
Non-polymers3965
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-33 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.807, 52.194, 97.491
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Zinc finger protein 524


Mass: 15589.205 Da / Num. of mol.: 1 / Fragment: Zinc Finger 1-4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF524 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96C55

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*G)-3')


Mass: 4745.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*C)-3')


Mass: 4433.902 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 95 molecules

#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Imidazole malate, pH 5.5, 15% (w/ v) polyethylene glycol 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 9248 / % possible obs: 99.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Χ2: 0.831 / Net I/σ(I): 11.7 / Num. measured all: 61403
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.444.70.3774190.9040.1890.4230.8389.5
2.44-2.495.40.3434380.9380.1610.3810.85999.8
2.49-2.535.60.2884580.9580.1310.3170.834100
2.53-2.5960.2514510.9640.1110.2750.855100
2.59-2.646.30.2264540.9730.0960.2460.898100
2.64-2.770.2134550.9690.0860.230.871100
2.7-2.777.40.1854620.9780.0720.1990.877100
2.77-2.857.40.1664460.9790.0640.1780.887100
2.85-2.937.20.1374580.9840.0540.1470.91100
2.93-3.027.20.1154440.9870.0460.1240.836100
3.02-3.137.20.0944790.9950.0370.1010.889100
3.13-3.267.40.0774550.9990.0330.0840.91899.6
3.26-3.417.10.0614650.9960.0270.0670.89599.8
3.41-3.586.70.0554580.9970.0230.060.90199.6
3.58-3.817.20.0514600.9980.020.0550.93199.8
3.81-4.16.90.0464700.9960.0190.050.82699.8
4.1-4.526.70.0414710.9980.0170.0440.712100
4.52-5.176.90.0384750.9980.0150.0410.618100
5.17-6.516.60.0384970.9980.0160.0410.644100
6.51-505.80.0365330.9980.0160.0390.62999.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→27.587 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 447 4.88 %
Rwork0.2183 8715 -
obs0.2201 9162 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.98 Å2 / Biso mean: 38.1981 Å2 / Biso min: 24.18 Å2
Refinement stepCycle: final / Resolution: 2.4→27.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 609 12 90 1639
Biso mean--34.67 33.78 -
Num. residues----143
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.7470.3731380.2915284399
2.747-3.45990.2841460.2458286399
3.4599-27.5870.21181630.18413009100

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