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- PDB-8gn4: The crystal structure of ZBTB10 ZF1-2 R767Q in complex with telom... -

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Basic information

Entry
Database: PDB / ID: 8gn4
TitleThe crystal structure of ZBTB10 ZF1-2 R767Q in complex with telomeric DNA TTAGGG
Components
  • DNA (5'-D(*AP*TP*AP*TP*AP*AP*CP*CP*CP*TP*A)-3')
  • DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*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 / nucleus / metal ion binding
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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: DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*TP*A)-3')
C: DNA (5'-D(*AP*TP*AP*TP*AP*AP*CP*CP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7985
Polymers14,6673
Non-polymers1312
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-20 kcal/mol
Surface area6930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.866, 32.665, 36.105
Angle α, β, γ (deg.)105.990, 90.460, 105.210
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 7962.536 Da / Num. of mol.: 1 / Mutation: R767Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96DT7
#2: DNA chain DNA (5'-D(*TP*TP*AP*GP*GP*GP*TP*TP*AP*TP*A)-3')


Mass: 3403.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*TP*AP*TP*AP*AP*CP*CP*CP*TP*A)-3')


Mass: 3301.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Cacodylate, pH 6.5, 27 % v/v PEG 2000 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: Jun 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 9392 / % possible obs: 91.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.024 / Rrim(I) all: 0.046 / Χ2: 0.863 / Net I/σ(I): 9 / Num. measured all: 31985
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.932.70.33560.9050.2010.3621.19871.5
1.93-1.972.80.2974040.9150.1980.3590.98679.2
1.97-2.0130.2744220.9310.1790.3280.99382.9
2.01-2.052.90.1984340.9670.1330.240.98785.4
2.05-2.093.10.2024610.9560.1310.2421.05788.3
2.09-2.143.30.224880.9470.1380.2611.05595.9
2.14-2.193.50.1695010.9670.1040.1991.07296.9
2.19-2.253.50.1474920.9820.0890.1730.95997
2.25-2.323.40.1394900.9770.0860.1640.93796.6
2.32-2.393.40.1085110.9850.0660.1270.87296.8
2.39-2.483.40.0964780.9830.0590.1130.98293.2
2.48-2.583.60.0774950.9920.0460.090.88492.9
2.58-2.73.60.0674730.9940.040.0780.8696.9
2.7-2.843.70.0574890.9940.0340.0660.77996.3
2.84-3.023.70.0494970.9960.0290.0570.8595.6
3.02-3.253.50.0334620.9990.020.0380.76390.8
3.25-3.583.70.0254960.9990.0150.0290.70996.1
3.58-4.093.70.0284890.9980.0170.0330.67795.3
4.09-5.153.60.0264810.9980.0150.030.56492.1
5.15-403.70.0234730.9980.0140.0270.49593.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GN3

8gn3


Resolution: 1.9→30.188 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 29.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 438 4.9 %
Rwork0.2102 8502 -
obs0.2125 8940 87.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.17 Å2 / Biso mean: 24.6561 Å2 / Biso min: 9.59 Å2
Refinement stepCycle: final / Resolution: 1.9→30.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms441 445 2 100 988
Biso mean--15.31 32.89 -
Num. residues----75
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9003-2.17520.29121290.2664235173
2.1752-2.74020.28481560.2377310395
2.7402-30.1880.23641530.1827304894
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)
12.283-1.1738-0.90471.93772.21343.90530.10410.09190.0748-0.0414-0.0018-0.1085-0.0652-0.1371-0.08520.0798-0.02050.02020.05350.0280.14777.4103-6.83313.7955
21.5339-0.03081.66790.9916-0.93993.96990.23230.19770.00230.14450.11810.1351-0.35790.09470.00910.18220.02570.0870.2040.05760.2003-0.5633-10.684410.7708
31.9334-0.0171-0.41710.89480.3261.24340.2625-0.00760.13180.07940.02020.0718-0.23850.2559-0.03180.1755-0.04410.04790.19180.00310.078-0.5808-9.21818.9011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 720 through 772)A720 - 772
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 11)B1 - 11
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 11)C1 - 11

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