+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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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 pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / positive regulation of norepinephrine uptake / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / intracellular glucocorticoid receptor signaling pathway / cellular response to cytochalasin B ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / positive regulation of norepinephrine uptake / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / intracellular glucocorticoid receptor signaling pathway / cellular response to cytochalasin B / bBAF complex / blastocyst hatching / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / morphogenesis of a polarized epithelium / Formation of annular gap junctions / neural retina development / GBAF complex / Gap junction degradation / postsynaptic actin cytoskeleton / protein localization to adherens junction / regulation of G0 to G1 transition / dense body / Cell-extracellular matrix interactions / Tat protein binding / XY body / nucleosome disassembly / Folding of actin by CCT/TriC / regulation of double-strand break repair / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Ino80 complex / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / hepatocyte differentiation / blastocyst formation / Prefoldin mediated transfer of substrate to CCT/TriC / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / RNA polymerase I preinitiation complex assembly / N-acetyltransferase activity / positive regulation by host of viral transcription / tight junction / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / ATP-dependent chromatin remodeler activity / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / positive regulation of double-strand break repair / germ cell nucleus / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / cellular response to fatty acid / apical junction complex / nuclear androgen receptor binding / regulation of chromosome organization / maintenance of blood-brain barrier / establishment or maintenance of cell polarity / nuclear chromosome / spinal cord development / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / positive regulation of stem cell population maintenance / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Recycling pathway of L1 / androgen receptor signaling pathway / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / negative regulation of cell differentiation / brush border / regulation of embryonic development / kinesin binding / calyx of Held / positive regulation of Wnt signaling pathway / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / intracellular estrogen receptor signaling pathway / regulation of DNA repair / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / regulation of protein localization to plasma membrane / DNA polymerase binding / transcription initiation-coupled chromatin remodeling / positive regulation of DNA repair / EPHB-mediated forward signaling / substantia nigra development 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 | He S / Wu Z / Tian Y / Yu Z / Yu J / Wang X / Li J / Liu B / Xu Y | |||||||||
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 | 35.4 KB 35.4 KB | Display Display | EMDB header |
Images | emd_0974.png | 8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0974 ftp://ftp.pdbj.org/pub/emdb/structures/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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
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 |