+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 / blastocyst hatching / bBAF complex / 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 / morphogenesis of a polarized epithelium / negative regulation of androgen receptor signaling pathway / neural retina development / GBAF complex / postsynaptic actin cytoskeleton / protein localization to adherens junction / Formation of annular gap junctions / regulation of G0 to G1 transition / dense body / Gap junction degradation / Tat protein binding / XY body / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of double-strand break repair / Ino80 complex / nucleosome disassembly / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / hepatocyte differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / blastocyst formation / 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 / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / ATP-dependent chromatin remodeler activity / 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 / establishment or maintenance of cell polarity / maintenance of blood-brain barrier / nuclear chromosome / spinal cord development / positive regulation of stem cell population maintenance / positive regulation of double-strand break repair via homologous recombination / cortical cytoskeleton / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / nitric-oxide synthase binding / androgen receptor signaling pathway / regulation of cyclin-dependent protein serine/threonine kinase activity / Recycling pathway of L1 / 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 / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / regulation of DNA repair / regulation of protein localization to plasma membrane / DNA polymerase binding / transcription initiation-coupled chromatin remodeling / EPHB-mediated forward signaling / positive regulation of DNA repair / 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 |