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- PDB-8gn3: The crystal structure of ZBTB10 ZF1-2 in complex with telomeric v... -

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Basic information

Entry
Database: PDB / ID: 8gn3
TitleThe crystal structure of ZBTB10 ZF1-2 in complex with telomeric vairant repeat TTGGGG
Components
  • DNA (5'-D(*AP*TP*AP*CP*AP*AP*CP*CP*CP*CP*A)-3')
  • DNA (5'-D(*TP*TP*GP*GP*GP*GP*TP*TP*GP*TP*A)-3')
  • Zinc finger and BTB domain-containing protein 10
KeywordsDNA BINDING PROTEIN/DNA / Telomeric DNA binding / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


telomeric DNA binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / chromosome, telomeric region / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
C2H2-type zinc-finger domain / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc finger and BTB domain-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsLi, F.D. / Wang, S.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1932122 China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural insights into the recognition of telomeric variant repeat TTGGGG by broad-complex, tramtrack and bric-a-brac - zinc finger protein ZBTB10.
Authors: Wang, S. / Xu, Z. / Li, M. / Lv, M. / Shen, S. / Shi, Y. / Li, F.
History
DepositionAug 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 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_ASTM / _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

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Assembly

Deposited unit
A: Zinc finger and BTB domain-containing protein 10
B: Zinc finger and BTB domain-containing protein 10
C: DNA (5'-D(*TP*TP*GP*GP*GP*GP*TP*TP*GP*TP*A)-3')
D: DNA (5'-D(*AP*TP*AP*CP*AP*AP*CP*CP*CP*CP*A)-3')
E: DNA (5'-D(*TP*TP*GP*GP*GP*GP*TP*TP*GP*TP*A)-3')
F: DNA (5'-D(*AP*TP*AP*CP*AP*AP*CP*CP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,65810
Polymers29,3966
Non-polymers2624
Water4,270237
1
A: Zinc finger and BTB domain-containing protein 10
C: DNA (5'-D(*TP*TP*GP*GP*GP*GP*TP*TP*GP*TP*A)-3')
D: DNA (5'-D(*AP*TP*AP*CP*AP*AP*CP*CP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8295
Polymers14,6983
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-25 kcal/mol
Surface area7010 Å2
MethodPISA
2
B: Zinc finger and BTB domain-containing protein 10
E: DNA (5'-D(*TP*TP*GP*GP*GP*GP*TP*TP*GP*TP*A)-3')
F: DNA (5'-D(*AP*TP*AP*CP*AP*AP*CP*CP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8295
Polymers14,6983
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-25 kcal/mol
Surface area7510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.119, 82.304, 82.389
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Zinc finger and BTB domain-containing protein 10 / Zinc finger protein RIN ZF


Mass: 7991.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB10, RINZF, RINZFC / Production host: Escherichia coli (E. coli) / References: UniProt: Q96DT7
#2: DNA chain DNA (5'-D(*TP*TP*GP*GP*GP*GP*TP*TP*GP*TP*A)-3')


Mass: 3435.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*TP*AP*CP*AP*AP*CP*CP*CP*CP*A)-3')


Mass: 3271.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium HEPES, pH 8.2, 40 % v/v PEG 500 MME

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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: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 23647 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.063 / Χ2: 0.928 / Net I/σ(I): 6.9 / Num. measured all: 297558
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8310.31.14511440.70.3621.2040.9499.4
1.83-1.8611.71.02411130.770.3061.0710.9399.8
1.86-1.912.50.85311980.8750.2470.8890.92799.9
1.9-1.9412.80.74811500.8880.2140.7780.947100
1.94-1.9812.90.6411440.9230.1840.6670.932100
1.98-2.0312.60.55111690.9350.160.5740.948100
2.03-2.0811.70.42811760.9540.1290.4481.005100
2.08-2.1313.50.37311740.9720.1050.3880.9999.9
2.13-2.213.40.28311550.9830.0790.2940.97999.9
2.2-2.2713.30.25311790.9860.0710.2631.075100
2.27-2.3512.90.20111700.9880.0580.2091.003100
2.35-2.4412.70.15611950.9930.0450.1630.961100
2.44-2.5512.10.12911650.9950.0380.1350.99899.9
2.55-2.6913.40.10711680.9970.030.1110.98499.9
2.69-2.8613.20.08411860.9980.0240.0880.956100
2.86-3.08130.06511980.9980.0180.0670.946100
3.08-3.3912.20.04511840.9990.0130.0470.945100
3.39-3.8813.40.035122410.010.0370.88100
3.88-4.8812.10.0312370.9990.0090.0310.73199.9
4.88-40120.023131810.0070.0240.49699.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→33.08 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 1106 4.86 %
Rwork0.2 21673 -
obs0.2013 22779 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.22 Å2 / Biso mean: 23.5228 Å2 / Biso min: 6.53 Å2
Refinement stepCycle: final / Resolution: 1.8→33.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 890 4 237 2088
Biso mean--12.74 28.84 -
Num. residues----161
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.8820.3036950.2396214378
1.882-1.98120.25671210.2228270898
1.9812-2.10530.24341360.21642769100
2.1053-2.26780.25341460.20592747100
2.2678-2.49590.25181490.21482765100
2.4959-2.85690.251760.21112751100
2.8569-3.59870.21121530.18742838100
3.5987-33.080.17861300.18252952100

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