+Open data
-Basic information
Entry | Database: PDB / ID: 6lth | ||||||
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Title | Structure of human BAF Base module | ||||||
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 glucose mediated signaling pathway / H3K9me3 modified histone binding / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex ...negative regulation of myeloid progenitor cell differentiation / single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / H3K9me3 modified histone binding / bBAF complex / negative regulation of androgen receptor signaling pathway / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex / Tat protein binding / blastocyst hatching / GBAF complex / neural retina development / regulation of G0 to G1 transition / N-acetyltransferase activity / EGR2 and SOX10-mediated initiation of Schwann cell myelination / hepatocyte differentiation / regulation of nucleotide-excision repair / RSC-type complex / XY body / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / germ cell nucleus / positive regulation of double-strand break repair / positive regulation of T cell differentiation / cellular response to fatty acid / ATP-dependent chromatin remodeler activity / nuclear androgen receptor binding / nuclear chromosome / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / DNA polymerase binding / Interleukin-7 signaling / neurogenesis / transcription initiation-coupled chromatin remodeling / apoptotic signaling pathway / transcription coregulator binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / nuclear receptor binding / helicase activity / positive regulation of cell differentiation / positive regulation of DNA-binding transcription factor activity / transcription coregulator activity / lysine-acetylated histone binding / Formation of the beta-catenin:TCF transactivating complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of cell growth / kinetochore / fibrillar center / RMTs methylate histone arginines / positive regulation of miRNA transcription / DNA integration / nuclear matrix / transcription corepressor activity / p53 binding / positive regulation of cold-induced thermogenesis / nervous system development / histone binding / molecular adaptor activity / transcription coactivator activity / hydrolase activity / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / signaling receptor binding / negative regulation of DNA-templated transcription / centrosome / chromatin binding / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular space / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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 | 6lth.cif.gz | 459.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lth.ent.gz | 299.6 KB | Display | PDB format |
PDBx/mmJSON format | 6lth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lth_validation.pdf.gz | 750.6 KB | Display | wwPDB validaton report |
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Full document | 6lth_full_validation.pdf.gz | 780.8 KB | Display | |
Data in XML | 6lth_validation.xml.gz | 56 KB | Display | |
Data in CIF | 6lth_validation.cif.gz | 83.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/6lth ftp://data.pdbj.org/pub/pdb/validation_reports/lt/6lth | HTTPS FTP |
-Related structure data
Related structure data | 0968MC 0969C 0970C 0971C 0972C 0973C 0974C 6ltjC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 5 molecules ILNOR
#1: 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 | ||
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#2: Protein | Mass: 242250.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARID1A / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: O14497 | ||
#4: 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 #7: Protein | | Mass: 44222.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPF2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q92785 |
-SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily ... , 3 types, 3 molecules MPQ
#3: Protein | Mass: 44199.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCB1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q12824 |
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#5: 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 |
#6: 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 |
-Non-polymers , 1 types, 1 molecules
#8: 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
Component | Name: Structure of human BAF Base module / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
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Molecular weight | Units: KILODALTONS/NANOMETER / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293T |
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 |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 32 / Used frames/image: 1-32 |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197606 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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