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Yorodumi- EMDB-31925: The motor-nucleosome module of human chromatin remodeling PBAF-nu... -
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- Basic information
Basic information
| Entry |  | |||||||||
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| Title | The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex | |||||||||
|  Map data | The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex | |||||||||
|  Sample | 
 | |||||||||
|  Keywords | complex / DNA BINDING PROTEIN | |||||||||
| Function / homology |  Function and homology information positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / neural retina development / npBAF complex / nBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome array spacer activity / GBAF complex ...positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / neural retina development / npBAF complex / nBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome array spacer activity / GBAF complex / regulation of G0 to G1 transition / Tat protein binding / RNA polymerase I preinitiation complex assembly / RSC-type complex / ATP-dependent chromatin remodeler activity / regulation of nucleotide-excision repair / host-mediated activation of viral transcription / nucleosome disassembly / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear androgen receptor binding / positive regulation of double-strand break repair / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / positive regulation of signal transduction by p53 class mediator / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / Chromatin modifying enzymes / DNA polymerase binding / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / transcription coregulator binding / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / helicase activity / Formation of the beta-catenin:TCF transactivating complex / negative regulation of cell growth / kinetochore / positive regulation of miRNA transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RMTs methylate histone arginines / nuclear matrix / fibrillar center / p53 binding / structural constituent of chromatin / transcription corepressor activity / nucleosome / heterochromatin formation / nervous system development / nucleosome assembly / positive regulation of cold-induced thermogenesis / histone binding / transcription coactivator activity / hydrolase activity / chromatin remodeling / protein heterodimerization activity / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / membrane Similarity search - Function | |||||||||
| Biological species |  Homo sapiens (human) /  Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
|  Authors | Chen ZC / Chen KJ | |||||||||
| 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
Structure visualization
| Supplemental images | 
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- Downloads & links
Downloads & links
-EMDB archive
| Map data |  emd_31925.map.gz | 9.6 MB |  EMDB map data format | |
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| Header (meta data) |  emd-31925-v30.xml  emd-31925.xml | 21.6 KB 21.6 KB | Display Display |  EMDB header | 
| Images |  emd_31925.png | 111 KB | ||
| Filedesc metadata |  emd-31925.cif.gz | 7.5 KB | ||
| Archive directory |  http://ftp.pdbj.org/pub/emdb/structures/EMD-31925  ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31925 | HTTPS FTP | 
-Validation report
| Summary document |  emd_31925_validation.pdf.gz | 343.4 KB | Display |  EMDB validaton report | 
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| Full document |  emd_31925_full_validation.pdf.gz | 343 KB | Display | |
| Data in XML |  emd_31925_validation.xml.gz | 6.8 KB | Display | |
| Data in CIF |  emd_31925_validation.cif.gz | 7.9 KB | Display | |
| Arichive directory |  https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31925  ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31925 | HTTPS FTP | 
-Related structure data
| Related structure data |  7vdtMC  7vdvC M: atomic model generated by this map C: citing same article ( | 
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| Similar structure data | Similarity search - Function & homology  F&H Search | 
- Links
Links
| EMDB pages |  EMDB (EBI/PDBe) /  EMDataResource | 
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| Related items in Molecule of the Month | 
- Map
Map
| File |  Download / File: emd_31925.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | The motor-nucleosome module of human chromatin remodeling PBAF-nucleosome complex | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
 
 Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| 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
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: Isoform 2 of Transcription activator BRG1
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #5: Histone H3
+Macromolecule #6: DNA (207-MER)
+Macromolecule #7: DNA (207-MER)
+Macromolecule #8: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM | 
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|  Processing | single particle reconstruction | 
| Aggregation state | particle | 
- Sample preparation
Sample preparation
| Buffer | pH: 7.5 | 
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| Vitrification | Cryogen name: ETHANE | 
- Electron microscopy
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 | 
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 Escherichia coli (E. coli)
Escherichia coli (E. coli)

