+Open data
-Basic information
Entry | Database: PDB / ID: 7egm | ||||||
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Title | The SRM module of SWI/SNF-nucleosome complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Chromatin remodeler complex | ||||||
Function / homology | Function and homology information carbon catabolite activation of transcription from RNA polymerase II promoter / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / aggrephagy / rDNA binding / HDACs deacetylate histones / DNA strand invasion / RSC-type complex / SUMOylation of chromatin organization proteins ...carbon catabolite activation of transcription from RNA polymerase II promoter / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / aggrephagy / rDNA binding / HDACs deacetylate histones / DNA strand invasion / RSC-type complex / SUMOylation of chromatin organization proteins / SWI/SNF complex / ATP-dependent chromatin remodeler activity / nuclear chromosome / positive regulation of transcription by RNA polymerase I / ATP-dependent activity, acting on DNA / nucleosomal DNA binding / lysine-acetylated histone binding / maturation of LSU-rRNA / cellular response to amino acid starvation / helicase activity / nucleotide-excision repair / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via homologous recombination / chromatin DNA binding / DNA-templated DNA replication / structural constituent of chromatin / double-strand break repair / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / chromatin remodeling / hydrolase activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Chen, Z.C. / Chen, K.J. / He, Z.Y. / Ye, Y.P. | ||||||
Citation | Journal: Cell Discov / Year: 2021 Title: Structure of the SWI/SNF complex bound to the nucleosome and insights into the functional modularity. Authors: Zhenyu He / Kangjing Chen / Youpi Ye / Zhucheng Chen / | ||||||
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 | 7egm.cif.gz | 517 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7egm.ent.gz | 374.9 KB | Display | PDB format |
PDBx/mmJSON format | 7egm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7egm_validation.pdf.gz | 760.4 KB | Display | wwPDB validaton report |
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Full document | 7egm_full_validation.pdf.gz | 794.9 KB | Display | |
Data in XML | 7egm_validation.xml.gz | 65.1 KB | Display | |
Data in CIF | 7egm_validation.cif.gz | 99.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/7egm ftp://data.pdbj.org/pub/pdb/validation_reports/eg/7egm | HTTPS FTP |
-Related structure data
Related structure data | 31136MC 7eg6C 7egpC 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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-Components
-Transcription regulatory protein ... , 3 types, 3 molecules AHI
#1: Protein | Mass: 114311.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: SNF2, GAM1, RIC1, SWI2, TYE3, YOR290C Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P22082, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#5: Protein | Mass: 63947.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: SNF12, SWP73, YNR023W, N3224 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P53628 |
#6: Protein | Mass: 37652.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: SNF6, YHL025W Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P18888 |
-SWI/SNF chromatin-remodeling complex subunit ... , 2 types, 2 molecules BC
#2: Protein | Mass: 124885.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: SWI1, ADR6, GAM3, YPL016W, LPA1 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P09547 |
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#3: Protein | Mass: 103954.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: SNF5, SWI10, TYE4, YBR289W, YBR2036 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P18480 |
-Protein , 2 types, 3 molecules DEJ
#4: Protein | Mass: 94178.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: SWI3, TYE2, YJL176C, J0495 Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P32591 #7: Protein | | Mass: 71510.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: SWP82, YFL049W Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) References: UniProt: P43554 |
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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: Substrate Recruitment Module of Chromatin remodeler complex SWI/SNF Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
Source (recombinant) | Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210422 / Symmetry type: POINT |