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Yorodumi- EMDB-31926: The overall structure of human chromatin remodeling PBAF-nucleoso... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31926 | |||||||||
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Title | The overall structure of human chromatin remodeling PBAF-nucleosome complex | |||||||||
Map data | The structure of human chromatin remodeling PBAF-nucleosome complex | |||||||||
Sample |
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Function / homology | Function and homology information single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / 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 / regulation of transepithelial transport / blastocyst hatching / morphogenesis of a polarized epithelium / bBAF complex ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / 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 / 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 / coronary artery morphogenesis / 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 / cardiac muscle cell proliferation / cellular response to fatty acid / nuclear androgen receptor binding / establishment or maintenance of cell polarity / negative regulation of G1/S transition of mitotic cell cycle / nuclear chromosome / regulation of cyclin-dependent protein serine/threonine kinase activity / spinal cord development / maintenance of blood-brain barrier / homeostatic process / 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 / regulation of mitotic cell cycle / 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 / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / embryonic organ development / neurogenesis / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / heart morphogenesis Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Xenopus laevis (African clawed frog) / unidentified (others) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Chen ZC / Chen KJ / Yuan JJ | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nature / Year: 2022 Title: Structure of human chromatin-remodelling PBAF complex bound to a nucleosome. Authors: Junjie Yuan / Kangjing Chen / Wenbo Zhang / Zhucheng Chen / Abstract: DNA wraps around the histone octamer to form nucleosomes, the repeating unit of chromatin, which create barriers for accessing genetic information. Snf2-like chromatin remodellers couple the energy ...DNA wraps around the histone octamer to form nucleosomes, the repeating unit of chromatin, which create barriers for accessing genetic information. Snf2-like chromatin remodellers couple the energy of ATP binding and hydrolysis to reposition and recompose the nucleosome, and have vital roles in various chromatin-based transactions. Here we report the cryo-electron microscopy structure of the 12-subunit human chromatin-remodelling polybromo-associated BRG1-associated factor (PBAF) complex bound to the nucleosome. The motor subunit SMARCA4 engages the nucleosome in the active conformation, which reveals clustering of multiple disease-associated mutations at the interfaces that are essential for chromatin-remodelling activity. SMARCA4 recognizes the H2A-H2B acidic pocket of the nucleosome through three arginine anchors of the Snf2 ATP coupling (SnAc) domain. PBAF shows notable functional modularity, and most of the auxiliary subunits are interwoven into three lobe-like submodules for nucleosome recognition. The PBAF-specific auxiliary subunit ARID2 acts as the structural core for assembly of the DNA-binding lobe, whereas PBRM1, PHF10 and BRD7 are collectively incorporated into the lobe for histone tail binding. Together, our findings provide mechanistic insights into nucleosome recognition by PBAF and a structural basis for understanding SMARCA4-related human diseases. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31926.map.gz | 12.4 MB | EMDB map data format | |
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Header (meta data) | emd-31926-v30.xml emd-31926.xml | 36.6 KB 36.6 KB | Display Display | EMDB header |
Images | emd_31926.png | 132.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31926 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31926 | HTTPS FTP |
-Validation report
Summary document | emd_31926_validation.pdf.gz | 336.6 KB | Display | EMDB validaton report |
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Full document | emd_31926_full_validation.pdf.gz | 336.2 KB | Display | |
Data in XML | emd_31926_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_31926_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31926 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31926 | HTTPS FTP |
-Related structure data
Related structure data | 7vdvMC 7vdtC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31926.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The structure of human chromatin remodeling PBAF-nucleosome complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : The motor-nucleosome module of human chromatin remodeling PBAF-nu...
+Supramolecule #1: The motor-nucleosome module of human chromatin remodeling PBAF-nu...
+Macromolecule #1: Histone H4
+Macromolecule #2: Histone H2A
+Macromolecule #3: Histone H2B 1.1
+Macromolecule #4: Histone H3
+Macromolecule #7: Isoform 2 of Transcription activator BRG1
+Macromolecule #8: Actin-like protein 6A
+Macromolecule #9: Actin, cytoplasmic 1
+Macromolecule #10: AT-rich interactive domain-containing protein 2,AT-rich interacti...
+Macromolecule #11: PHD finger protein 10
+Macromolecule #12: Isoform 2 of Bromodomain-containing protein 7
+Macromolecule #13: unknown
+Macromolecule #14: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
+Macromolecule #15: SWI/SNF complex subunit SMARCC2
+Macromolecule #16: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
+Macromolecule #17: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
+Macromolecule #18: Protein polybromo-1
+Macromolecule #19: unknown
+Macromolecule #5: DNA (207-MER)
+Macromolecule #6: DNA (207-MER)
+Macromolecule #20: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #21: MAGNESIUM ION
+Macromolecule #22: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 137659 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |