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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0974 | |||||||||
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Title | Structure of nucleosome-bound human BAF complex | |||||||||
![]() | Structure of nucleosome-bound human BAF complex in the apo state | |||||||||
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![]() | Chromatin remodeler / Complex / GENE REGULATION | |||||||||
Function / homology | ![]() 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 / cellular response to cytochalasin B / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / nuclear receptor-mediated glucocorticoid signaling pathway ...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 / cellular response to cytochalasin B / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / nuclear receptor-mediated glucocorticoid signaling pathway / regulation of transepithelial transport / morphogenesis of a polarized epithelium / blastocyst hatching / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / brahma complex / nBAF complex / protein localization to adherens junction / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / GBAF complex / neural retina development / dense body / regulation of G0 to G1 transition / Formation of annular gap junctions / Gap junction degradation / Cell-extracellular matrix interactions / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Folding of actin by CCT/TriC / apical protein localization / hepatocyte differentiation / regulation of double-strand break repair / regulation of nucleotide-excision repair / Ino80 complex / adherens junction assembly / XY body / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / blastocyst formation / RHOF GTPase cycle / RNA polymerase I preinitiation complex assembly / 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 / regulation of mitotic metaphase/anaphase transition / nucleosome disassembly / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / ATP-dependent chromatin remodeler activity / positive regulation of double-strand break repair / germ cell nucleus / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / cellular response to fatty acid / establishment or maintenance of cell polarity / nuclear androgen receptor binding / nuclear chromosome / regulation of cyclin-dependent protein serine/threonine kinase activity / spinal cord development / regulation of chromosome organization / cortical cytoskeleton / maintenance of blood-brain barrier / 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 double-strand break repair via homologous recombination / positive regulation of Wnt signaling pathway / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / 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 / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / EPHB-mediated forward signaling / substantia nigra development / positive regulation of DNA repair Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Shuang H / Zihan W | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 475.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 35.8 KB 35.8 KB | Display Display | ![]() |
Images | ![]() | 8 KB | ||
Filedesc metadata | ![]() | 11.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 662.5 KB | Display | ![]() |
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Full document | ![]() | 662.1 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 9.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ltjMC ![]() 0968C ![]() 0969C ![]() 0970C ![]() 0971C ![]() 0972C ![]() 0973C ![]() 6lthC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 % |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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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 |