[English] 日本語
![](img/lk-miru.gif)
- EMDB-31926: The overall structure of human chromatin remodeling PBAF-nucleoso... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The overall structure of human chromatin remodeling PBAF-nucleosome complex | |||||||||
![]() | The structure of human chromatin remodeling PBAF-nucleosome complex | |||||||||
![]() |
| |||||||||
Function / homology | ![]() single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / 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 / morphogenesis of a polarized epithelium / blastocyst hatching ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / 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 / morphogenesis of a polarized epithelium / blastocyst hatching / bBAF complex / postsynaptic actin cytoskeleton organization / protein localization to adherens junction / postsynaptic actin cytoskeleton / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / npBAF complex / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / brahma complex / nBAF complex / 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 / Folding of actin by CCT/TriC / EGR2 and SOX10-mediated initiation of Schwann cell myelination / apical protein localization / regulation of double-strand break repair / coronary artery morphogenesis / nucleosome disassembly / Ino80 complex / regulation of nucleotide-excision repair / hepatocyte differentiation / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / XY body / blastocyst formation / RHOF GTPase cycle / RSC-type complex / 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 / Sensory processing of sound by inner hair cells of the cochlea / ATP-dependent chromatin remodeler activity / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / germ cell nucleus / positive regulation of T cell differentiation / cardiac muscle cell proliferation / cellular response to fatty acid / apical junction complex / nuclear androgen receptor binding / establishment or maintenance of cell polarity / negative regulation of G1/S transition of mitotic cell cycle / regulation of cyclin-dependent protein serine/threonine kinase activity / nuclear chromosome / spinal cord development / regulation of chromosome organization / cortical cytoskeleton / maintenance of blood-brain barrier / homeostatic process / 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 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 / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / embryonic organ development / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / heart morphogenesis / histone acetyltransferase activity / nucleosomal DNA binding / transcription initiation-coupled chromatin remodeling Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Chen ZC / Chen KJ / Yuan JJ | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 12.4 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 36.6 KB 36.6 KB | Display Display | ![]() |
Images | ![]() | 132.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 336.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 336.2 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vdvMC ![]() 7vdtC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | The structure of human chromatin remodeling PBAF-nucleosome complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.0825 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-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 |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: ![]() |
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 |
---|---|
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |