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- PDB-7egm: The SRM module of SWI/SNF-nucleosome complex -

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Basic information

Entry
Database: PDB / ID: 7egm
TitleThe SRM module of SWI/SNF-nucleosome complex
Components
  • (SWI/SNF chromatin-remodeling complex subunit ...) x 2
  • (Transcription regulatory protein ...) x 3
  • SWI/SNF complex subunit SWI3
  • SWI/SNF global transcription activator complex subunit SWP82
KeywordsDNA BINDING PROTEIN / Chromatin remodeler complex
Function / homology
Function and homology information


carbon catabolite activation of transcription / 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 / DNA strand invasion / HDACs deacetylate histones / rDNA binding / nucleosome array spacer activity / RSC-type complex ...carbon catabolite activation of transcription / 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 / DNA strand invasion / HDACs deacetylate histones / rDNA binding / nucleosome array spacer activity / RSC-type complex / ATP-dependent chromatin remodeler activity / SUMOylation of chromatin organization proteins / SWI/SNF complex / nucleosomal DNA binding / nuclear chromosome / positive regulation of transcription by RNA polymerase I / histone reader activity / histone H4 reader activity / maturation of LSU-rRNA / : / transcription initiation-coupled chromatin remodeling / cellular response to amino acid starvation / nucleotide-excision repair / helicase activity / double-strand break repair via homologous recombination / chromatin DNA binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 / hydrolase activity / chromatin remodeling / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus / cytosol
Similarity search - Function
Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / : / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. ...Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / : / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / Helicase/SANT-associated domain / HSA domain profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / SWIB/MDM2 domain superfamily / SANT domain profile. / SANT domain / Myb-like DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SWI/SNF chromatin-remodeling complex subunit SWI1 / SWI/SNF chromatin-remodeling complex subunit SNF5 / Transcription regulatory protein SNF6 / Transcription regulatory protein SNF2 / SWI/SNF complex subunit SWI3 / SWI/SNF global transcription activator complex subunit SWP82 / Transcription regulatory protein SNF12
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChen, Z.C. / Chen, K.J. / He, Z.Y. / Ye, Y.P.
CitationJournal: 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
DepositionMar 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Transcription regulatory protein SNF2
B: SWI/SNF chromatin-remodeling complex subunit SWI1
C: SWI/SNF chromatin-remodeling complex subunit SNF5
D: SWI/SNF complex subunit SWI3
H: Transcription regulatory protein SNF12
I: Transcription regulatory protein SNF6
J: SWI/SNF global transcription activator complex subunit SWP82
E: SWI/SNF complex subunit SWI3


Theoretical massNumber of molelcules
Total (without water)704,6208
Polymers704,6208
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Transcription regulatory protein ... , 3 types, 3 molecules AHI

#1: Protein Transcription regulatory protein SNF2 / ATP-dependent helicase SNF2 / Regulatory protein GAM1 / Regulatory protein SWI2 / SWI/SNF complex ...ATP-dependent helicase SNF2 / Regulatory protein GAM1 / Regulatory protein SWI2 / SWI/SNF complex component SNF2 / Transcription factor TYE3


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
#5: Protein Transcription regulatory protein SNF12 / SWI/SNF complex component SWP73


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 Transcription regulatory protein SNF6 / SWI/SNF complex component SNF6


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

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SWI/SNF chromatin-remodeling complex subunit ... , 2 types, 2 molecules BC

#2: Protein SWI/SNF chromatin-remodeling complex subunit SWI1 / Regulatory protein GAM3 / SWI/SNF complex subunit SWI1 / Transcription regulatory protein ADR6 / ...Regulatory protein GAM3 / SWI/SNF complex subunit SWI1 / Transcription regulatory protein ADR6 / Transcription regulatory protein SWI1


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
#3: Protein SWI/SNF chromatin-remodeling complex subunit SNF5 / SWI/SNF complex subunit SNF5 / Transcription factor TYE4 / Transcription regulatory protein SNF5


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

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Protein , 2 types, 3 molecules DEJ

#4: Protein SWI/SNF complex subunit SWI3 / Transcription factor TYE2 / Transcription regulatory protein SWI3


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 SWI/SNF global transcription activator complex subunit SWP82


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Substrate Recruitment Module of Chromatin remodeler complex SWI/SNF
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210422 / Symmetry type: POINT

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