[English] 日本語
Yorodumi
- PDB-6lth: Structure of human BAF Base module -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lth
TitleStructure of human BAF Base module
Components
  • (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ...) x 3
  • AT-rich interactive domain-containing protein 1A
  • SWI/SNF complex subunit SMARCC2
  • Transcription activator BRG1
  • Zinc finger protein ubi-d4
KeywordsGENE REGULATION / Chromatin remodeler / Complex
Function / homology
Function and homology information


optic cup formation involved in camera-type eye development / cardiac chamber development / negative regulation of myeloid progenitor cell differentiation / H3K9me3 modified histone binding / formation of primary germ layer / single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of histone H3-K9 dimethylation / maintenance of chromatin silencing / positive regulation of glucose mediated signaling pathway / brahma complex ...optic cup formation involved in camera-type eye development / cardiac chamber development / negative regulation of myeloid progenitor cell differentiation / H3K9me3 modified histone binding / formation of primary germ layer / single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of histone H3-K9 dimethylation / maintenance of chromatin silencing / positive regulation of glucose mediated signaling pathway / brahma complex / npBAF complex / positive regulation of histone H4 acetylation / nBAF complex / glucocorticoid receptor signaling pathway / neural retina development / negative regulation of androgen receptor signaling pathway / Tat protein binding / nucleosome mobilization / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / RNA polymerase I core promoter sequence-specific DNA binding / positive regulation of histone H3-K9 acetylation / cardiac muscle cell differentiation / placenta blood vessel development / nucleosome disassembly / SWI/SNF complex / positive regulation by host of viral transcription / nucleosome binding / neurogenesis / chromatin-mediated maintenance of transcription / toxin transport / ATP-dependent chromatin remodeling / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / stem cell population maintenance / cellular response to fatty acid / beta-catenin-TCF complex assembly / negative regulation of histone H3-K9 trimethylation / N-acetyltransferase activity / positive regulation of Wnt signaling pathway / molecular adaptor activity / interleukin-7-mediated signaling pathway / DNA-dependent ATPase activity / histone acetyltransferase complex / intracellular estrogen receptor signaling pathway / DNA polymerase binding / positive regulation of pri-miRNA transcription by RNA polymerase II / helicase activity / histone acetyltransferase activity / forebrain development / embryo implantation / androgen receptor signaling pathway / nuclear chromosome / androgen receptor binding / nuclear receptor binding / lysine-acetylated histone binding / apoptotic signaling pathway / fibrillar center / neural tube closure / nervous system development / transcription corepressor activity / negative regulation of cell growth / DNA integration / p53 binding / chromatin organization / histone binding / protein N-terminus binding / positive regulation of DNA-binding transcription factor activity / chromatin remodeling / transcription coactivator activity / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / centrosome / regulation of transcription by RNA polymerase II / intracellular membrane-bounded organelle / nuclear chromatin / signaling receptor binding / apoptotic process / transcription factor binding / negative regulation of transcription, DNA-templated / nucleolus / chromatin binding / positive regulation of transcription, DNA-templated / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / DNA binding / extracellular space / membrane / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol
N-terminal domain of DPF2/REQ. / Helicase, C-terminal / Chromatin-remodeling complex component Sfh1/SNF5 / SANT domain / Bromodomain, conserved site / Zinc finger, PHD-finger / SWIB domain / SWI/SNF-like complex subunit BAF250/Osa / P-loop containing nucleoside triphosphate hydrolase / Glutamine-Leucine-Glutamine, QLQ ...N-terminal domain of DPF2/REQ. / Helicase, C-terminal / Chromatin-remodeling complex component Sfh1/SNF5 / SANT domain / Bromodomain, conserved site / Zinc finger, PHD-finger / SWIB domain / SWI/SNF-like complex subunit BAF250/Osa / P-loop containing nucleoside triphosphate hydrolase / Glutamine-Leucine-Glutamine, QLQ / Snf2, ATP coupling domain / SWI/SNF complex subunit BAF57 / SWI/SNF-like complex subunit BAF250a / SWI/SNF complex subunit BRG1 / SMARCC, SWIRM-associated domain / SMARCC, N-terminal / Armadillo-type fold / Helicase/SANT-associated domain / SWI/SNF-like complex subunit BAF250, C-terminal / BRK domain / Bromodomain / SANT/Myb domain / Chromo/chromo shadow domain / SNF2-related, N-terminal domain / Zinc finger, PHD-type / SWIB/MDM2 domain / SNF5/SMARCB1/INI1 / Helicase superfamily 1/2, ATP-binding domain / SWIRM domain / Homeobox-like domain superfamily / High mobility group box domain / Zinc finger, FYVE/PHD-type / Armadillo-like helical / Zinc finger, RING/FYVE/PHD-type / Zinc finger C2H2-type / SMARCC, C-terminal / Requiem/DPF N-terminal domain / Zinc finger C2H2 superfamily / SNF5 / SMARCB1 / INI1 / HSA / BRK domain / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Winged helix-like DNA-binding domain superfamily / SWI/SNF-like complex subunit BAF250/Osa / Myb-like DNA-binding domain / Helicase conserved C-terminal domain / SWIRM domain / SWIRM-associated region 1 / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / SWIB/MDM2 domain / HMG (high mobility group) box / PHD-finger / Bromodomain / ARID/BRIGHT DNA binding domain / ARID DNA-binding domain / SNF2-like, N-terminal domain superfamily / SWIB/MDM2 domain superfamily / High mobility group box domain superfamily / BRK domain superfamily / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWI/SNF complex subunit SMARCC2 / ARID DNA-binding domain superfamily / Bromodomain-like superfamily / BRCT domain superfamily / SNF2 family N-terminal domain
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / AT-rich interactive domain-containing protein 1A / Transcription activator BRG1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / Zinc finger protein ubi-d4 / SWI/SNF complex subunit SMARCC2
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsShuang, H. / Zihan, W. / Yuan, T. / Zishuo, Y. / Jiali, Y. / Xinxin, W. / Jie, L. / Bijun, L. / Yanhui, X.
CitationJournal: Science / Year: 2020
Title: Structure of nucleosome-bound human BAF complex.
Authors: Shuang He / Zihan Wu / Yuan Tian / Zishuo Yu / Jiali Yu / Xinxin Wang / Jie Li / Bijun Liu / Yanhui Xu /
Abstract: Mammalian SWI/SNF family chromatin remodelers, BAF and PBAF, regulate chromatin structure and transcription, with their mutations linked to cancers. The 3.7 Å-resolution cryo-EM structure of human ...Mammalian SWI/SNF family chromatin remodelers, BAF and PBAF, regulate chromatin structure and transcription, with their mutations linked to cancers. The 3.7 Å-resolution cryo-EM structure of human BAF bound to nucleosome reveals that the nucleosome is sandwiched by the Base and the ATPase modules, which are bridged by the actin-related protein (ARP) module. The ATPase motor is positioned proximal to nucleosomal DNA and, upon ATP hydrolysis, would engage with and pump DNA along the nucleosome. The C-terminal α-helix of SMARCB1, enriched in positively charged residues frequently mutated in cancers, mediates interactions with an acidic patch of nucleosome. ARID1A and SMARCC serve as a structural core and scaffold in the Base module organization, respectively. Our study provides structural insights into subunit organization and nucleosome recognition of human BAF complex.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJan 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0968
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
I: Transcription activator BRG1
L: AT-rich interactive domain-containing protein 1A
M: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
N: SWI/SNF complex subunit SMARCC2
O: SWI/SNF complex subunit SMARCC2
P: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Q: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
R: Zinc finger protein ubi-d4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)886,7799
Polymers886,7148
Non-polymers651
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area55610 Å2
ΔGint-360 kcal/mol
Surface area83310 Å2

-
Components

-
Protein , 4 types, 5 molecules ILNOR

#1: Protein Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4


Mass: 184923.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein AT-rich interactive domain-containing protein 1A / ARID domain-containing protein 1A


Mass: 242250.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARID1A / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O14497
#4: Protein SWI/SNF complex subunit SMARCC2 / / BRG1-associated factor 170 / BAF170 / SWI/SNF complex 170 kDa subunit / SWI/SNF-related matrix- ...BRG1-associated factor 170 / BAF170 / SWI/SNF complex 170 kDa subunit / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 2


Mass: 133048.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCC2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8TAQ2
#7: Protein Zinc finger protein ubi-d4 /


Mass: 44222.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q92785

-
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ... , 3 types, 3 molecules MPQ

#3: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Mass: 44199.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCB1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q12824
#5: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1


Mass: 58311.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCD1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q96GM5
#6: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1


Mass: 46710.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCE1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q969G3

-
Non-polymers , 1 types, 1 molecules

#8: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Structure of human BAF Base module / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7 / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 32 / Used frames/image: 1-32

-
Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4Gctf1.06CTF correction
7UCSF Chimera1.13model fitting
9cryoSPARC2.12.4initial Euler assignment
10RELION3.0.8final Euler assignment
11RELION3.0.8classification
12cryoSPARC2.12.43D reconstruction
13PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197606 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00515266
f_angle_d0.66420605
f_dihedral_angle_d9.2239418
f_chiral_restr0.0432302
f_plane_restr0.0052653

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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