+Open data
-Basic information
Entry | Database: PDB / ID: 6ltj | ||||||
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Title | Structure of nucleosome-bound human BAF complex | ||||||
Components |
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Keywords | GENE REGULATION / Chromatin remodeler / Complex | ||||||
Function / homology | Function and homology information 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 / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / glucocorticoid receptor signaling pathway / blastocyst hatching ...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 / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / glucocorticoid receptor signaling pathway / blastocyst hatching / cellular response to cytochalasin B / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / morphogenesis of a polarized epithelium / neural retina development / Formation of annular gap junctions / GBAF complex / Gap junction degradation / postsynaptic actin cytoskeleton / protein localization to adherens junction / regulation of G0 to G1 transition / dense body / Cell-extracellular matrix interactions / Tat protein binding / XY body / nucleosome disassembly / Folding of actin by CCT/TriC / regulation of double-strand break repair / EGR2 and SOX10-mediated initiation of Schwann cell myelination / Ino80 complex / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / hepatocyte differentiation / blastocyst formation / Prefoldin mediated transfer of substrate to CCT/TriC / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / RNA polymerase I preinitiation complex assembly / N-acetyltransferase activity / positive regulation by host of viral transcription / tight junction / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / ATP-dependent chromatin remodeler activity / Interaction between L1 and Ankyrins / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / positive regulation of double-strand break repair / germ cell nucleus / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / cellular response to fatty acid / apical junction complex / nuclear androgen receptor binding / regulation of chromosome organization / maintenance of blood-brain barrier / establishment or maintenance of cell polarity / nuclear chromosome / spinal cord development / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / positive regulation of stem cell population maintenance / nitric-oxide synthase binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Recycling pathway of L1 / androgen receptor signaling pathway / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / negative regulation of cell differentiation / brush border / regulation of embryonic development / kinesin binding / calyx of Held / positive regulation of Wnt signaling pathway / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / intracellular estrogen receptor signaling pathway / regulation of DNA repair / ATP-dependent activity, acting on DNA / regulation of protein localization to plasma membrane / Chromatin modifying enzymes / DNA polymerase binding / transcription initiation-coupled chromatin remodeling / positive regulation of DNA repair / EPHB-mediated forward signaling / substantia nigra development Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | He, S. / Wu, Z. / Tian, Y. / Yu, Z. / Yu, J. / Wang, X. / Li, J. / Liu, B. / Xu, Y. | ||||||
Citation | Journal: Science / Year: 2020 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ltj.cif.gz | 860.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ltj.ent.gz | 648.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ltj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/6ltj ftp://data.pdbj.org/pub/pdb/validation_reports/lt/6ltj | HTTPS FTP |
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-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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6PI79 #2: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62799 #3: Protein | Mass: 13993.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06897 #4: Protein | Mass: 13873.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: H2B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q92131, UniProt: P02281*PLUS #5: Protein | | Mass: 184923.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) 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.) Homo sapiens (human) / Gene: ACTL6A, BAF53, BAF53A / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O96019 #7: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P60709 #8: Protein | | Mass: 142316.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARID1A, BAF250, BAF250A / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O14497 #10: Protein | Mass: 133048.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCC2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q8TAQ2 #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.) Homo sapiens (human) / Gene: DPF2, BAF45D / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q92785 |
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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.) Homo sapiens (human) / Gene: SMARCB1, BAF47 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q12824 |
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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.) Homo sapiens (human) / Gene: SMARCD1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q96GM5 |
#12: Protein | Mass: 46710.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCE1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q969G3 |
-DNA chain , 2 types, 2 molecules XY
#14: DNA chain | Mass: 36520.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#15: DNA chain | Mass: 36929.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 1 types, 1 molecules
#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 |
-Sample preparation
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO | ||||||||||||||||||||||||
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Source (recombinant) |
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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 % |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-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 |