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- EMDB-0968: Structure of human BAF Base module -

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Entry
Database: EMDB / ID: EMD-0968
TitleStructure of human BAF Base module
Map data
SampleStructure of nucleosome-bound human BAF Base module
Function / homology
Function and homology information


optic cup formation involved in camera-type eye development / cardiac chamber development / formation of primary germ layer / H3K9me3 modified histone binding / negative regulation of myeloid progenitor cell differentiation / 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 / formation of primary germ layer / H3K9me3 modified histone binding / negative regulation of myeloid progenitor cell differentiation / 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 / glycosaminoglycan catabolic process / glucocorticoid receptor signaling pathway / neural retina development / negative regulation of androgen receptor signaling pathway / glycosaminoglycan biosynthetic process / 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 / dendrite morphogenesis / 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 / regulation of dendrite morphogenesis / 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 / retinoid metabolic process / apoptotic signaling pathway / lysosomal lumen / PDZ domain binding / fibrillar center / neural tube closure / ephrin receptor signaling pathway / nervous system development / transcription corepressor activity / negative regulation of cell growth / cell migration / Golgi lumen / DNA integration / p53 binding / chromatin organization / post-translational protein modification / collagen-containing extracellular matrix / histone binding / protein N-terminus binding / positive regulation of DNA-binding transcription factor activity / leukocyte migration / 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 / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / nuclear chromatin / signaling receptor binding / apoptotic process / transcription factor binding / negative regulation of transcription, DNA-templated / nucleolus / chromatin binding / cellular protein metabolic process / positive regulation of transcription, DNA-templated / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / protein-containing complex
Zinc finger C2H2-type / Helicase superfamily 1/2, ATP-binding domain / SWI/SNF-like complex subunit BAF250/Osa / SWIB domain / Chromo/chromo shadow domain / Zinc finger, PHD-finger / SANT/Myb domain / Bromodomain, conserved site / SANT domain / Chromatin-remodeling complex component Sfh1/SNF5 ...Zinc finger C2H2-type / Helicase superfamily 1/2, ATP-binding domain / SWI/SNF-like complex subunit BAF250/Osa / SWIB domain / Chromo/chromo shadow domain / Zinc finger, PHD-finger / SANT/Myb domain / Bromodomain, conserved site / SANT domain / Chromatin-remodeling complex component Sfh1/SNF5 / Armadillo-type fold / Glutamine-Leucine-Glutamine, QLQ / Helicase/SANT-associated domain / Syndecan / P-loop containing nucleoside triphosphate hydrolase / Zinc finger, RING/FYVE/PHD-type / Armadillo-like helical / Zinc finger, FYVE/PHD-type / High mobility group box domain / Homeobox-like domain superfamily / SWIRM domain / SNF5/SMARCB1/INI1 / Bromodomain / ARID DNA-binding domain / BRK domain / Neurexin/syndecan/glycophorin C / SWIB/MDM2 domain / Helicase, C-terminal / Requiem/DPF N-terminal domain / Syndecan/Neurexin domain / Winged helix-like DNA-binding domain superfamily / SNF2-like, N-terminal domain superfamily / SWI/SNF complex subunit SMARCC2 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 / BRK domain superfamily / High mobility group box domain superfamily / SWIB/MDM2 domain superfamily / ARID DNA-binding domain superfamily / Bromodomain-like superfamily / SNF2-related, N-terminal domain / Snf2, ATP coupling domain / BRCT domain superfamily / Zinc finger C2H2 superfamily / SWI/SNF-like complex subunit BAF250, C-terminal / SWI/SNF complex subunit BAF57 / SWI/SNF-like complex subunit BAF250a / SWI/SNF complex subunit BRG1 / Syndecan, conserved site / Syndecan-2 / SMARCC, N-terminal / SMARCC, SWIRM-associated domain / SMARCC, C-terminal / Zinc finger, PHD-type
AT-rich interactive domain-containing protein 1A / Syndecan-2 / Transcription activator BRG1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / SWI/SNF complex subunit SMARCC2 / Zinc finger protein ubi-d4 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1
Biological speciesHomo sapiens (human)
Methodsingle 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 ReportPDB-ID: 6ith

SummaryFull report
PDB-ID: 6lth

SummaryFull report
About validation report
History
DepositionJan 21, 2020-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
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  • Surface view colored by radius
  • Surface level: 1
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  • Surface view with fitted model
  • Atomic models: : PDB-6lth
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0968.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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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: 1 / Movie #1: 1
Minimum - Maximum-2.3567643 - 4.937579
Average (Standard dev.)0.0014853961 (±0.045854725)
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-2.3574.9380.001

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Supplemental data

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Sample components

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Entire Structure of nucleosome-bound human BAF Base module

EntireName: Structure of nucleosome-bound human BAF Base module / Number of components: 1

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Component #1: protein, Structure of nucleosome-bound human BAF Base module

ProteinName: Structure of nucleosome-bound human BAF Base module / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Experimental details

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Sample preparation

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

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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)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 197606
3D reconstructionSoftware: cryoSPARC / Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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