[English] 日本語
Yorodumi
- PDB-6yxo: Structure of the N-terminal module of the human SWI/SNF-subunit B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yxo
TitleStructure of the N-terminal module of the human SWI/SNF-subunit BAF155/SMARCC1
ComponentsSWI/SNF complex subunit SMARCC1
KeywordsSIGNALING PROTEIN / Baf155 / SWI/SNF-subunit
Function / homology
Function and homology information


prostate gland development / Formation of the embryonic stem cell BAF (esBAF) complex / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the polybromo-BAF (pBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / GBAF complex ...prostate gland development / Formation of the embryonic stem cell BAF (esBAF) complex / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Formation of the polybromo-BAF (pBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / GBAF complex / regulation of G0 to G1 transition / RSC-type complex / XY body / regulation of nucleotide-excision repair / nucleosome disassembly / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / positive regulation of double-strand break repair / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / positive regulation of myoblast differentiation / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / animal organ morphogenesis / male germ cell nucleus / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / kinetochore / nuclear matrix / RMTs methylate histone arginines / insulin receptor signaling pathway / nervous system development / histone binding / transcription coactivator activity / chromatin remodeling / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / SMARCC, C-terminal / SWIRM-associated region 1 / SWIRM domain / SWIRM domain ...SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / SMARCC, C-terminal / SWIRM-associated region 1 / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / BRCT domain superfamily / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
SWI/SNF complex subunit SMARCC1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsAllen, M.D. / Bycroft, M. / Zinzalla, G.
CitationJournal: Commun Biol / Year: 2021
Title: SWI/SNF subunit BAF155 N-terminus structure informs the impact of cancer-associated mutations and reveals a potential drug binding site.
Authors: Allen, M.D. / Freund, S.M.V. / Bycroft, M. / Zinzalla, G.
History
DepositionMay 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SWI/SNF complex subunit SMARCC1
B: SWI/SNF complex subunit SMARCC1


Theoretical massNumber of molelcules
Total (without water)65,4122
Polymers65,4122
Non-polymers00
Water6,071337
1
A: SWI/SNF complex subunit SMARCC1


Theoretical massNumber of molelcules
Total (without water)32,7061
Polymers32,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SWI/SNF complex subunit SMARCC1


Theoretical massNumber of molelcules
Total (without water)32,7061
Polymers32,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.810, 136.815, 56.042
Angle α, β, γ (deg.)90.00, 110.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein SWI/SNF complex subunit SMARCC1 / BRG1-associated factor 155 / BAF155 / SWI/SNF complex 155 kDa subunit / SWI/SNF-related matrix- ...BRG1-associated factor 155 / BAF155 / SWI/SNF complex 155 kDa subunit / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1


Mass: 32706.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCC1, BAF155 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q92922
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2 M Magnesium formate (pH 5.9), 20% PEG 3350. Protein at 16 mg/ml.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.975456 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975456 Å / Relative weight: 1
ReflectionResolution: 2→49.01 Å / Num. obs: 41433 / % possible obs: 99.5 % / Redundancy: 5.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.05 / Rrim(I) all: 0.086 / Net I/σ(I): 10.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5994 / CC1/2: 0.899 / Rpim(I) all: 0.306 / Rrim(I) all: 0.533 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→49.005 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 2121 5.13 %
Rwork0.1973 --
obs0.1993 41380 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→49.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 0 0 337 4819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064612
X-RAY DIFFRACTIONf_angle_d0.6286250
X-RAY DIFFRACTIONf_dihedral_angle_d2.622758
X-RAY DIFFRACTIONf_chiral_restr0.042648
X-RAY DIFFRACTIONf_plane_restr0.004802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04660.34391490.29552540X-RAY DIFFRACTION99
2.0466-2.09780.2831490.27192617X-RAY DIFFRACTION100
2.0978-2.15450.30721490.24612616X-RAY DIFFRACTION100
2.1545-2.21790.2741570.24882614X-RAY DIFFRACTION100
2.2179-2.28950.28621170.23932628X-RAY DIFFRACTION100
2.2895-2.37130.2941230.24482619X-RAY DIFFRACTION100
2.3713-2.46620.26941440.24292615X-RAY DIFFRACTION100
2.4662-2.57850.27811440.23792647X-RAY DIFFRACTION100
2.5785-2.71440.27361510.2322605X-RAY DIFFRACTION100
2.7144-2.88440.25721530.22992616X-RAY DIFFRACTION100
2.8844-3.10710.23381450.21722626X-RAY DIFFRACTION100
3.1071-3.41970.25961540.19942606X-RAY DIFFRACTION99
3.4197-3.91440.21091240.17762625X-RAY DIFFRACTION99
3.9144-4.9310.19371310.15082624X-RAY DIFFRACTION99
4.931-49.0050.19611310.16152661X-RAY DIFFRACTION99

+
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