[English] 日本語
Yorodumi
- EMDB-0974: Structure of nucleosome-bound human BAF complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0974
TitleStructure of nucleosome-bound human BAF complex
Map data
SampleStructure of nucleosome-bound human BAF complex
  • Nucleosome
  • BAF
  • Histone H3.3H3F3A
  • Histone H4
  • Histone H2A type 1
  • Histone H2B
  • Transcription activator BRG1
  • Actin-like protein 6A
  • Actin, cytoplasmic 1
  • AT-rich interactive domain-containing protein 1A
  • (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ...) x 3
  • SWI/SNF complex subunit SMARCC2
  • Zinc finger protein ubi-d4
  • (nucleic-acidNucleic acid) x 2
  • ligand
Function / homology
Function and homology information


optic cup formation involved in camera-type eye development / cardiac chamber development / H3K9me3 modified histone binding / negative regulation of myeloid progenitor cell differentiation / formation of primary germ layer / single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of histone H3-K9 dimethylation / positive regulation of norepinephrine uptake / maintenance of chromatin silencing / brahma complex ...optic cup formation involved in camera-type eye development / cardiac chamber development / H3K9me3 modified histone binding / negative regulation of myeloid progenitor cell differentiation / formation of primary germ layer / single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of histone H3-K9 dimethylation / positive regulation of norepinephrine uptake / maintenance of chromatin silencing / brahma complex / positive regulation of glucose mediated signaling pathway / npBAF complex / cellular response to cytochalasin B / regulation of transepithelial transport / positive regulation of histone H4 acetylation / nBAF complex / protein localization to adherens junction / morphogenesis of a polarized epithelium / histone H2A acetylation / glucocorticoid receptor signaling pathway / neural retina development / structural constituent of postsynaptic actin cytoskeleton / postsynaptic actin cytoskeleton / blastocyst formation / negative regulation of androgen receptor signaling pathway / dense body / Tat protein binding / nucleosome mobilization / postsynaptic actin cytoskeleton organization / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / regulation of norepinephrine uptake / RNA polymerase I core promoter sequence-specific DNA binding / positive regulation of histone H3-K9 acetylation / apical protein localization / cardiac muscle cell differentiation / placenta blood vessel development / Ino80 complex / nucleosome disassembly / adherens junction assembly / SWI/SNF complex / tight junction / positive regulation by host of viral transcription / NuA4 histone acetyltransferase complex / nucleosome binding / positive regulation of gene expression, epigenetic / apical junction complex / neurogenesis / cell junction assembly / 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 / kinesin binding / establishment or maintenance of cell polarity / stem cell population maintenance / regulation of growth / cellular response to fatty acid / nitric-oxide synthase binding / spinal cord development / cortical cytoskeleton / beta-catenin-TCF complex assembly / negative regulation of histone H3-K9 trimethylation / N-acetyltransferase activity / synaptic vesicle endocytosis / histone H4 acetylation / positive regulation of Wnt signaling pathway / regulation of cyclin-dependent protein serine/threonine kinase activity / molecular adaptor activity / interleukin-7-mediated signaling pathway / DNA-dependent ATPase activity / histone acetyltransferase complex / intracellular estrogen receptor signaling pathway / DNA polymerase binding / calyx of Held / positive regulation of pri-miRNA transcription by RNA polymerase II / adherens junction / cell motility / regulation of protein localization to plasma membrane / substantia nigra development / helicase activity / histone acetyltransferase activity / regulation of transmembrane transporter activity / forebrain development / embryo implantation / androgen receptor signaling pathway / axonogenesis / nuclear chromosome / androgen receptor binding / DNA-templated transcription, initiation / presynapse / actin filament / structural constituent of cytoskeleton / nuclear receptor binding / lysine-acetylated histone binding / apoptotic signaling pathway / platelet aggregation / fibrillar center / cytoplasmic ribonucleoprotein granule / Schaffer collateral - CA1 synapse / neural tube closure
Actin family / Histone H2A/H2B/H3 / Bromodomain, conserved site / SANT domain / Chromatin-remodeling complex component Sfh1/SNF5 / Armadillo-type fold / Glutamine-Leucine-Glutamine, QLQ / Helicase/SANT-associated domain / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type ...Actin family / Histone H2A/H2B/H3 / Bromodomain, conserved site / SANT domain / Chromatin-remodeling complex component Sfh1/SNF5 / Armadillo-type fold / Glutamine-Leucine-Glutamine, QLQ / Helicase/SANT-associated domain / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / Armadillo-like helical / Zinc finger, FYVE/PHD-type / Histone-fold / High mobility group box domain / Homeobox-like domain superfamily / SWIRM domain / SNF5/SMARCB1/INI1 / Histone H4, conserved site / ARID DNA-binding domain / Histone H3/CENP-A / SNF2-related, N-terminal domain / Histone H2B / Chromo/chromo shadow domain / SANT/Myb domain / Bromodomain / Helicase, C-terminal / BRK domain / Histone H4 / Zinc finger, PHD-type / Histone H2A / SWIB/MDM2 domain / Actin, conserved site / TATA box binding protein associated factor (TAF) / Zinc finger, PHD-finger / Zinc finger C2H2-type / SWIB domain / Histone H2A conserved site / 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 / SNF2-like, N-terminal domain superfamily / Bromodomain-like superfamily / Actin/actin-like conserved site / BRCT domain superfamily / Winged helix-like DNA-binding domain superfamily / Zinc finger C2H2 superfamily / CENP-T/Histone H4, histone fold / ARID DNA-binding domain superfamily / SWI/SNF-like complex subunit BAF250, C-terminal / Histone H2A, C-terminal domain / SMARCC, C-terminal / SWI/SNF-like complex subunit BAF250/Osa / Requiem/DPF N-terminal domain / P-loop containing nucleoside triphosphate hydrolase / 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 / SWIB/MDM2 domain superfamily
Histone H3.3 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / Zinc finger protein ubi-d4 / Histone H2B / SWI/SNF complex subunit SMARCC2 / Transcription activator BRG1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / Histone H4 / Actin, cytoplasmic 1 / Histone H2A type 1 ...Histone H3.3 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / Zinc finger protein ubi-d4 / Histone H2B / SWI/SNF complex subunit SMARCC2 / Transcription activator BRG1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / Histone H4 / Actin, cytoplasmic 1 / Histone H2A type 1 / Actin-like protein 6A / AT-rich interactive domain-containing protein 1A / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Biological speciesXenopus calcaratus (Biafran clawed frog) / Homo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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 ReportPDB-ID: 6ltj

SummaryFull reportAbout validation report
History
DepositionJan 22, 2020-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_0974.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 512 pix.
= 532.48 Å
1.04 Å/pix.
x 512 pix.
= 532.48 Å
1.04 Å/pix.
x 512 pix.
= 532.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.48 / Movie #1: 0.6
Minimum - Maximum-1.2884388 - 3.305587
Average (Standard dev.)-0.0000662169 (±0.107257016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 532.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z532.480532.480532.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.2883.306-0.000

-
Supplemental data

-
Sample components

+
Entire Structure of nucleosome-bound human BAF complex

EntireName: Structure of nucleosome-bound human BAF complex / Number of components: 19

+
Component #1: protein, Structure of nucleosome-bound human BAF complex

ProteinName: Structure of nucleosome-bound human BAF complex / Recombinant expression: No

+
Component #2: protein, Nucleosome

ProteinName: Nucleosome / Recombinant expression: No
SourceSpecies: Xenopus calcaratus (Biafran clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria) / Strain: BL21

+
Component #3: protein, BAF

ProteinName: BAF / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

+
Component #4: protein, Histone H3.3

ProteinName: Histone H3.3H3F3A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.360983 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

+
Component #5: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

+
Component #6: protein, Histone H2A type 1

ProteinName: Histone H2A type 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.993295 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

+
Component #7: protein, Histone H2B

ProteinName: Histone H2B / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.873086 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

+
Component #8: protein, Transcription activator BRG1

ProteinName: Transcription activator BRG1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 184.923828 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #9: protein, Actin-like protein 6A

ProteinName: Actin-like protein 6A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.236273 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #10: protein, Actin, cytoplasmic 1

ProteinName: Actin, cytoplasmic 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.78266 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #11: protein, AT-rich interactive domain-containing protein 1A

ProteinName: AT-rich interactive domain-containing protein 1A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 142.316531 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #12: protein, SWI/SNF-related matrix-associated actin-dependent regula...

ProteinName: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.015094 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #13: protein, SWI/SNF complex subunit SMARCC2

ProteinName: SWI/SNF complex subunit SMARCC2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 133.048109 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #14: protein, SWI/SNF-related matrix-associated actin-dependent regula...

ProteinName: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.311391 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #15: protein, SWI/SNF-related matrix-associated actin-dependent regula...

ProteinName: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.710371 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #16: protein, Zinc finger protein ubi-d4

ProteinName: Zinc finger protein ubi-d4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.781926 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #17: nucleic-acid, DNA (119-MER)

nucleic acidName: DNA (119-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG)(DG) (DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA)(DG) (DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA)(DC)(DC) (DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC) (DA)(DC)(DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC) (DT)(DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC) (DG)(DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG) (DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT) (DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)
MassTheoretical: 36.520266 kDa
SourceSpecies: Homo sapiens (human)

+
Component #18: nucleic-acid, DNA (119-MER)

nucleic acidName: DNA (119-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DA) (DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG)(DC) (DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA)(DC)(DG) (DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG) (DC)(DG)(DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG) (DC)(DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG) (DG)(DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC) (DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC) (DC)(DA)(DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)
MassTheoretical: 36.92952 kDa
SourceSpecies: Homo sapiens (human)

+
Component #19: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: OTHER
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 320658
3D reconstructionSoftware: RELION / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
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