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Open data
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Basic information
Entry | Database: PDB / ID: 6ltj | ||||||
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Title | Structure of nucleosome-bound human BAF complex | ||||||
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![]() | GENE REGULATION / Chromatin remodeler / Complex | ||||||
Function / homology | ![]() negative regulation of myeloid progenitor cell differentiation / 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 / 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 / regulation of transepithelial transport ...negative regulation of myeloid progenitor cell differentiation / 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 / 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 / regulation of transepithelial transport / nuclear receptor-mediated glucocorticoid signaling pathway / 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 / npBAF complex / negative regulation of androgen receptor signaling pathway / Tat protein binding / brahma complex / structural constituent of postsynaptic actin cytoskeleton / nBAF complex / GBAF complex / neural retina development / regulation of G0 to G1 transition / dense body / 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 / nucleosome disassembly / Ino80 complex / regulation of nucleotide-excision repair / adherens junction assembly / hepatocyte differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / XY body / blastocyst formation / RSC-type complex / RHOF GTPase cycle / Adherens junctions interactions / RNA polymerase I preinitiation complex assembly / N-acetyltransferase activity / tight junction / positive regulation by host of viral transcription / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / 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 / apical junction complex / cellular response to fatty acid / nuclear androgen receptor binding / establishment or maintenance of cell polarity / 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 / 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 / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / 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 / estrogen receptor signaling pathway / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / regulation of DNA repair / DNA polymerase binding / nucleosome binding / nucleosomal DNA binding / transcription initiation-coupled chromatin remodeling / EPHB-mediated forward signaling Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
![]() | He, S. / Wu, Z. / Tian, Y. / Yu, Z. / Yu, J. / Wang, X. / Li, J. / Liu, B. / Xu, Y. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Download
PDBx/mmCIF format | ![]() | 865.7 KB | Display | ![]() |
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PDB format | ![]() | 635.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 106.8 KB | Display | |
Data in CIF | ![]() | 162.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0974MC ![]() 0968C ![]() 0969C ![]() 0970C ![]() 0971C ![]() 0972C ![]() 0973C ![]() 6lthC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 10 types, 15 molecules AEBFCGDHIJKLNOR
#1: Protein | Mass: 15360.983 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 13993.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 13873.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | | Mass: 184923.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #6: Protein | | Mass: 45236.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #7: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #8: Protein | | Mass: 142316.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #10: Protein | Mass: 133048.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #13: Protein | | Mass: 32781.926 Da / Num. of mol.: 1 / Fragment: UNP residues 1-100, UNP residues 209-391 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ... , 3 types, 3 molecules MPQ
#9: Protein | Mass: 38015.094 Da / Num. of mol.: 1 / Fragment: UNP residues 1-113, UNP residues 172-385 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#11: Protein | Mass: 58311.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#12: Protein | Mass: 46710.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-DNA chain , 2 types, 2 molecules XY
#14: DNA chain | Mass: 36520.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#15: DNA chain | Mass: 36929.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/ZN.gif)
#16: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO | ||||||||||||||||||||||||
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software | Name: RELION / Version: 3.0.8 / Category: 3D reconstruction |
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CTF correction | Type: NONE |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 320658 / Symmetry type: POINT |