+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0974 | |||||||||
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Title | Structure of nucleosome-bound human BAF complex | |||||||||
Map data | Structure of nucleosome-bound human BAF complex in the apo state | |||||||||
Sample |
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Keywords | Chromatin remodeler / Complex / GENE REGULATION | |||||||||
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 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport ...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 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / regulation of transepithelial transport / blastocyst hatching / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / protein localization to adherens junction / brahma complex / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / dense body / Formation of annular gap junctions / regulation of G0 to G1 transition / neural retina development / Gap junction degradation / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / hepatocyte differentiation / regulation of double-strand break repair / adherens junction assembly / regulation of nucleotide-excision repair / Ino80 complex / XY body / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / blastocyst formation / RNA polymerase I preinitiation complex assembly / RHOF GTPase cycle / Regulation of MITF-M-dependent genes involved in pigmentation / N-acetyltransferase activity / Adherens junctions interactions / tight junction / positive regulation by host of viral transcription / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / 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 / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / cellular response to fatty acid / nuclear androgen receptor binding / establishment or maintenance of cell polarity / nuclear chromosome / regulation of cyclin-dependent protein serine/threonine kinase activity / spinal cord development / maintenance of blood-brain barrier / cortical cytoskeleton / regulation of chromosome organization / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of DNA replication / androgen receptor signaling pathway / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / regulation of embryonic development / positive regulation of Wnt signaling pathway / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / positive regulation of DNA repair / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / estrogen receptor signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / neurogenesis / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / transcription coregulator activity / lysine-acetylated histone binding Similarity search - Function | |||||||||
Biological species | Xenopus calcaratus (Biafran clawed frog) / Homo sapiens (human) / Xenopus laevis (African clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Shuang H / Zihan W | |||||||||
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_0974.map.gz | 475.5 MB | EMDB map data format | |
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Header (meta data) | emd-0974-v30.xml emd-0974.xml | 35.8 KB 35.8 KB | Display Display | EMDB header |
Images | emd_0974.png | 8 KB | ||
Filedesc metadata | emd-0974.cif.gz | 11.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0974 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0974 | HTTPS FTP |
-Validation report
Summary document | emd_0974_validation.pdf.gz | 662.5 KB | Display | EMDB validaton report |
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Full document | emd_0974_full_validation.pdf.gz | 662.1 KB | Display | |
Data in XML | emd_0974_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | emd_0974_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0974 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0974 | HTTPS FTP |
-Related structure data
Related structure data | 6ltjMC 0968C 0969C 0970C 0971C 0972C 0973C 6lthC 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_0974.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of nucleosome-bound human BAF complex in the apo state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 complex
+Supramolecule #1: Structure of nucleosome-bound human BAF complex
+Supramolecule #2: Nucleosome
+Supramolecule #3: BAF
+Macromolecule #1: Histone H3.3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B
+Macromolecule #5: Transcription activator BRG1
+Macromolecule #6: Actin-like protein 6A
+Macromolecule #7: Actin, cytoplasmic 1
+Macromolecule #8: AT-rich interactive domain-containing protein 1A
+Macromolecule #9: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
+Macromolecule #10: SWI/SNF complex subunit SMARCC2
+Macromolecule #11: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
+Macromolecule #12: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
+Macromolecule #13: Zinc finger protein ubi-d4
+Macromolecule #14: DNA (119-MER)
+Macromolecule #15: DNA (119-MER)
+Macromolecule #16: ZINC ION
-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 / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 320658 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |