[English] 日本語
Yorodumi
- PDB-7vrb: Structure of the Human BRG1/SS18 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vrb
TitleStructure of the Human BRG1/SS18 complex
ComponentsSMARCA4 protein,Protein SSXT
KeywordsONCOPROTEIN / four-helix bundle
Function / homology
Function and homology information


npBAF complex / neuronal stem cell population maintenance / GBAF complex / SWI/SNF complex / ATP-dependent chromatin remodeler activity / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / ephrin receptor signaling pathway / nuclear receptor coactivator activity ...npBAF complex / neuronal stem cell population maintenance / GBAF complex / SWI/SNF complex / ATP-dependent chromatin remodeler activity / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / ephrin receptor signaling pathway / nuclear receptor coactivator activity / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cell morphogenesis / microtubule cytoskeleton organization / microtubule cytoskeleton / histone binding / transcription coactivator activity / intracellular signal transduction / hydrolase activity / chromatin remodeling / response to xenobiotic stimulus / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
SS18, N-terminal / SS18 family / SSXT protein (N-terminal region) / SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ ...SS18, N-terminal / SS18 family / SSXT protein (N-terminal region) / SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SMARCA4 protein / Protein SSXT
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.389 Å
AuthorsCheng, Y. / Chen, F. / Zhou, H. / Long, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870750 China
National Natural Science Foundation of China (NSFC)31670758 China
CitationJournal: Nat Commun / Year: 2022
Title: Phase transition and remodeling complex assembly are important for SS18-SSX oncogenic activity in synovial sarcomas.
Authors: Cheng, Y. / Shen, Z. / Gao, Y. / Chen, F. / Xu, H. / Mo, Q. / Chu, X. / Peng, C.L. / McKenzie, T.T. / Palacios, B.E. / Hu, J. / Zhou, H. / Long, J.
History
DepositionOct 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: 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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SMARCA4 protein,Protein SSXT
B: SMARCA4 protein,Protein SSXT
C: SMARCA4 protein,Protein SSXT
D: SMARCA4 protein,Protein SSXT


Theoretical massNumber of molelcules
Total (without water)62,7594
Polymers62,7594
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, immunoprecipitation, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-45 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.607, 105.829, 225.857
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11B-52-

GLN

21D-219-

HOH

31D-235-

HOH

-
Components

#1: Protein
SMARCA4 protein,Protein SSXT / Protein SYT / Synovial sarcoma translocated to X chromosome protein


Mass: 15689.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: BRG1-SS18,BRG1-SS18 / Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, SS18, SSXT, SYT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9EGQ8, UniProt: Q15532
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.16 M sodium phosphate monobasic monohydrate and 0.24 M potassium phosphate dibasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.389→28.232 Å / Num. obs: 24275 / % possible obs: 99.9 % / Redundancy: 13.1 % / Rpim(I) all: 0.018 / Net I/σ(I): 39.16
Reflection shellResolution: 2.39→2.43 Å / Num. unique obs: 1205 / Rpim(I) all: 0.297

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.389→28.232 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 1274 5.29 %
Rwork0.2045 22810 -
obs0.207 24084 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.55 Å2 / Biso mean: 43.6616 Å2 / Biso min: 14.51 Å2
Refinement stepCycle: final / Resolution: 2.389→28.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 0 154 3547
Biso mean---42.98 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083446
X-RAY DIFFRACTIONf_angle_d0.8854646
X-RAY DIFFRACTIONf_chiral_restr0.045511
X-RAY DIFFRACTIONf_plane_restr0.006620
X-RAY DIFFRACTIONf_dihedral_angle_d15.6022152
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.389-2.48460.33681100.2535239994
2.4846-2.59760.30631520.23642518100
2.5976-2.73450.2891310.24582535100
2.7345-2.90560.29581430.23252543100
2.9056-3.12970.30151550.22142516100
3.1297-3.44420.25121240.20632571100
3.4442-3.94140.21431250.18242574100
3.9414-4.96140.20981650.17642565100
4.9614-6.480.23541690.1962258998

+
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