+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0968 | |||||||||
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Title | Structure of human BAF Base module | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / nuclear receptor-mediated glucocorticoid signaling pathway / blastocyst hatching / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / nuclear receptor-mediated glucocorticoid signaling pathway / blastocyst hatching / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex / Tat protein binding / GBAF complex / regulation of G0 to G1 transition / neural retina development / EGR2 and SOX10-mediated initiation of Schwann cell myelination / hepatocyte differentiation / regulation of nucleotide-excision repair / XY body / RSC-type complex / RNA polymerase I preinitiation complex assembly / Regulation of MITF-M-dependent genes involved in pigmentation / N-acetyltransferase activity / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / ATP-dependent chromatin remodeler activity / germ cell nucleus / positive regulation of double-strand break repair / positive regulation of T cell differentiation / cellular response to fatty acid / nuclear androgen receptor binding / nuclear chromosome / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / androgen receptor signaling pathway / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / estrogen receptor signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / neurogenesis / Chromatin modifying enzymes / DNA polymerase binding / transcription coregulator activity / lysine-acetylated histone binding / transcription coregulator binding / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / positive regulation of miRNA transcription / helicase activity / nuclear receptor binding / positive regulation of cell differentiation / apoptotic signaling pathway / Formation of the beta-catenin:TCF transactivating complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / positive regulation of DNA-binding transcription factor activity / negative regulation of cell growth / p53 binding / RMTs methylate histone arginines / kinetochore / fibrillar center / nuclear matrix / DNA integration / transcription corepressor activity / nervous system development / positive regulation of cold-induced thermogenesis / histone binding / transcription coactivator activity / molecular adaptor activity / chromatin remodeling / hydrolase activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / centrosome / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / nucleolus / apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular space / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 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, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to ...Mammalian SWI/SNF family chromatin remodelers, BRG1/BRM-associated factor (BAF) and polybromo-associated BAF (PBAF), regulate chromatin structure and transcription, and their mutations are linked to cancers. The 3.7-angstrom-resolution cryo-electron microscopy structure of human BAF bound to the nucleosome reveals that the nucleosome is sandwiched by the base and the adenosine triphosphatase (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, engages with and pumps 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 the nucleosome. AT-rich interactive domain-containing protein 1A (ARID1A) and the SWI/SNF complex subunit 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0968.map.gz | 25.3 MB | EMDB map data format | |
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Header (meta data) | emd-0968-v30.xml emd-0968.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
Images | emd_0968.png | 5.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0968 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0968 | HTTPS FTP |
-Validation report
Summary document | emd_0968_validation.pdf.gz | 291 KB | Display | EMDB validaton report |
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Full document | emd_0968_full_validation.pdf.gz | 290.6 KB | Display | |
Data in XML | emd_0968_validation.xml.gz | 8 KB | Display | |
Data in CIF | emd_0968_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0968 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0968 | HTTPS FTP |
-Related structure data
Related structure data | 6lthMC 0969C 0970C 0971C 0972C 0973C 0974C 6ltjC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0968.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Structure of nucleosome-bound human BAF Base module
Entire | Name: Structure of nucleosome-bound human BAF Base module |
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Components |
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-Supramolecule #1: Structure of nucleosome-bound human BAF Base module
Supramolecule | Name: Structure of nucleosome-bound human BAF Base module / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293T |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf (ver. 1.06) |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12.4) / Number images used: 197606 |
Initial angle assignment | Type: OTHER / Software - Name: cryoSPARC (ver. 2.12.4) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8) |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-6lth: |