[English] 日本語
Yorodumi
- PDB-7v9f: Selenomethionine mutant (L740Sem) of BEN4 domain of protein Bend3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v9f
TitleSelenomethionine mutant (L740Sem) of BEN4 domain of protein Bend3 with DNA
Components
  • BEN domain-containing protein 3
  • DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')
  • DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of ATP metabolic process / rDNA binding / rDNA heterochromatin formation / negative regulation of transcription by RNA polymerase I / heterochromatin / protein homooligomerization / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
BEN domain-containing protein 3 / BEN domain / BEN domain / BEN domain profile. / BEN
Similarity search - Domain/homology
CITRIC ACID / DNA / DNA (> 10) / BEN domain-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZhang, J. / Zhang, Y. / You, Q. / Huang, C. / Zhang, T. / Wang, M. / Zhang, T. / Yang, X. / Xiong, J. / Li, Y. ...Zhang, J. / Zhang, Y. / You, Q. / Huang, C. / Zhang, T. / Wang, M. / Zhang, T. / Yang, X. / Xiong, J. / Li, Y. / Liu, C.P. / Zhang, Z. / Xu, R.M. / Zhu, B.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508900, 2017YFA0504202 China
National Science Foundation (NSF, China)31991162, 31521002 China
Chinese Academy of SciencesXDB 37010100 China
CitationJournal: Science / Year: 2022
Title: Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation.
Authors: Zhang, J. / Zhang, Y. / You, Q. / Huang, C. / Zhang, T. / Wang, M. / Zhang, T. / Yang, X. / Xiong, J. / Li, Y. / Liu, C.P. / Zhang, Z. / Xu, R.M. / Zhu, B.
History
DepositionAug 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BEN domain-containing protein 3
B: DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')
C: DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8345
Polymers23,4503
Non-polymers3842
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-22 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.831, 96.831, 141.693
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1020-

HOH

21A-1026-

HOH

-
Components

#1: Protein BEN domain-containing protein 3


Mass: 13648.618 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bend3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6PAL0
#2: DNA chain DNA (5'-D(*TP*GP*GP*CP*CP*CP*CP*AP*CP*GP*CP*GP*GP*TP*GP*C)-3')


Mass: 4876.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*CP*AP*CP*CP*GP*CP*GP*TP*GP*GP*GP*GP*CP*CP*A)-3')


Mass: 4925.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 4.24 Å3/Da / Density % sol: 70.96 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate/Citric acid pH 4.0, 200 mM Sodium citrate tribasic, and 17% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 25183 / % possible obs: 99.8 % / Redundancy: 21 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 38.9
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 13812 / CC1/2: 0.082

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→41.153 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 1218 4.84 %
Rwork0.1775 23965 -
obs0.1797 25183 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.45 Å2 / Biso mean: 56.0472 Å2 / Biso min: 17.09 Å2
Refinement stepCycle: final / Resolution: 2.5→41.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 650 26 102 1670
Biso mean--67.48 48.45 -
Num. residues----139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051669
X-RAY DIFFRACTIONf_angle_d0.8142393
X-RAY DIFFRACTIONf_chiral_restr0.033261
X-RAY DIFFRACTIONf_plane_restr0.004198
X-RAY DIFFRACTIONf_dihedral_angle_d25.038688
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5003-2.60040.35541330.27712336135287
2.6004-2.71870.2571400.2537267399
2.7187-2.8620.34471400.2459270499
2.862-3.04130.28321490.2196268799
3.0413-3.2760.215820.18232748100
3.276-3.60550.20161790.15362677100
3.6055-4.12690.21961410.15612701100
4.1269-5.19780.14741390.14072719100
5.1978-41.1530.21841150.1584272099
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)
12.8817-0.71140.28880.70350.07920.8512-0.1153-0.00210.14030.01860.0124-0.21420.03810.304-0.0607-0.16740.05320.16420.9672-0.05180.185116.892937.86293.8953
23.11540.3872-0.18074.6501-0.16372.7511-0.0842-0.2223-0.49760.07090.06220.38090.4102-0.42880.07140.1099-0.17610.20440.78540.03290.3287-13.555725.7275-7.7726
33.83350.1437-0.51593.93330.00522.45720.0387-0.2781-0.150.29280.1917-0.13670.4950.2148-0.14460.55490.15280.17180.7622-0.06890.445212.242119.079710.1539
44.57830.624-2.43583.93040.37878.4396-0.14-0.2952-0.54330.0367-0.01460.26410.74350.18610.21320.43550.15580.13840.660.04980.461910.333619.02188.3629
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 712:789))A712 - 789
2X-RAY DIFFRACTION2chain 'A' and ((resseq 790:818))A790 - 818
3X-RAY DIFFRACTION3chain 'B'B1 - 16
4X-RAY DIFFRACTION4chain 'C'C1 - 16

+
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://pdbjlvh1.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