|Entry||Database: EMDB / ID: EMD-0968|
|Title||Structure of human BAF Base module|
|Sample||Structure 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 species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 3 Å|
|Authors||Shuang H / Zihan W / Yuan T / Zishuo Y / Jiali Y / Xinxin W / Jie L / Bijun L / Yanhui X|
|Citation||Journal: 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||PDB-ID: 6ith|
About validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_0968.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.04 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Structure of nucleosome-bound human BAF Base module
|Entire||Name: Structure of nucleosome-bound human BAF Base module / Number of components: 1|
-Component #1: protein, Structure of nucleosome-bound human BAF Base module
|Protein||Name: Structure of nucleosome-bound human BAF Base module / Recombinant expression: No|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Homo sapiens (human) / Cell of expression system: HEK293T|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 8|
|Vitrification||Cryogen name: ETHANE / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: OTHER|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 197606|
|3D reconstruction||Software: cryoSPARC / Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF|
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