[English] 日本語
Yorodumi
- PDB-8gn4: The crystal structure of ZBTB10 ZF1-2 R767Q in complex with telom... -

+
Open data


ID or keywords:

Loading...

-
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 / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / 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 / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more