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- PDB-7c4j: Cryo-EM structure of the yeast Swi/Snf complex in a nucleosome fr... -

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Basic information

Entry
Database: PDB / ID: 7c4j
TitleCryo-EM structure of the yeast Swi/Snf complex in a nucleosome free state
Components
  • (SWI/SNF chromatin-remodeling complex subunit ...) x 2
  • (Transcription regulatory protein ...) x 3
  • Actin-like protein ARP9
  • Actin-related protein 7
  • Regulator of Ty1 transposition protein 102
  • SWI/SNF complex subunit SWI3
  • SWI/SNF global transcription activator complex subunit SWP82
  • Unkown
KeywordsDNA BINDING PROTEIN / SWI/SNF remodeling / Swi-Snf complex / nucleosome
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 / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / positive regulation of invasive growth in response to glucose limitation / HDACs deacetylate histones / aggrephagy / Platelet degranulation ...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 / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / positive regulation of invasive growth in response to glucose limitation / HDACs deacetylate histones / aggrephagy / Platelet degranulation / DNA strand invasion / rDNA binding / : / SUMOylation of chromatin organization proteins / nucleosome disassembly / RSC-type complex / SWI/SNF complex / ATP-dependent chromatin remodeler activity / nucleosomal DNA binding / NuA4 histone acetyltransferase complex / nuclear chromosome / positive regulation of transcription by RNA polymerase I / ATP-dependent activity, acting on DNA / maturation of LSU-rRNA / helicase activity / chromosome segregation / transcription elongation by RNA polymerase II / nucleotide-excision repair / double-strand break repair via homologous recombination / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lysine-acetylated histone binding / DNA-templated DNA replication / chromatin DNA binding / double-strand break repair / chromatin organization / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / chromatin binding / chromatin / structural molecule activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / Glutamine-Leucine-Glutamine, QLQ / QLQ ...Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / 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 domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / DNA binding domain with preference for A/T rich regions / Helicase/SANT-associated domain / HSA domain profile. / AT hook, DNA-binding motif / ARID/BRIGHT DNA binding domain / SWIRM domain / SWIRM domain / SWIRM domain profile. / 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 / : / SANT domain profile. / SWIB/MDM2 domain superfamily / SANT domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Myb-like DNA-binding domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / ATPase, nucleotide binding domain / Actin / Actin family / Actin / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / ATPase, nucleotide binding domain / Bromodomain, conserved site / Bromodomain signature. / helicase superfamily c-terminal domain / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Nucleotidyltransferase; domain 5 / 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 / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
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 / Regulator of Ty1 transposition protein 102 / Transcription regulatory protein SNF12 / Actin-like protein ARP9 / Actin-related protein 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsWang, C.C. / Guo, Z.Y. / Zhan, X.C. / Zhang, X.F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
National Natural Science Foundation of China (NSFC)81920108015 China
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the yeast Swi/Snf complex in a nucleosome free state.
Authors: Chengcheng Wang / Zhouyan Guo / Xiechao Zhan / Fenghua Yang / Mingxuan Wu / Xiaofeng Zhang /
Abstract: SWI/SNF remodelers play a key role in regulating chromatin architecture and gene expression. Here, we report the cryo-EM structure of the Saccharomyces cerevisiae Swi/Snf complex in a nucleosome-free ...SWI/SNF remodelers play a key role in regulating chromatin architecture and gene expression. Here, we report the cryo-EM structure of the Saccharomyces cerevisiae Swi/Snf complex in a nucleosome-free state. The structure consists of a stable triangular base module and a flexible Arp module. The conserved subunits Swi1 and Swi3 form the backbone of the complex and closely interact with other components. Snf6, which is specific for yeast Swi/Snf complex, stabilizes the binding of the ATPase-containing subunit Snf2 to the base module. Comparison of the yeast Swi/Snf and RSC complexes reveals conserved structural features that govern the assembly and function of these two subfamilies of chromatin remodelers. Our findings complement those from recent structures of the yeast and human chromatin remodelers and provide further insights into the assembly and function of the SWI/SNF remodelers.
History
DepositionMay 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Transcription regulatory protein SNF12
B: SWI/SNF complex subunit SWI3
C: Transcription regulatory protein SNF6
D: SWI/SNF complex subunit SWI3
E: SWI/SNF global transcription activator complex subunit SWP82
F: SWI/SNF chromatin-remodeling complex subunit SNF5
H: Transcription regulatory protein SNF2
I: SWI/SNF chromatin-remodeling complex subunit SWI1
G: Unkown
J: Regulator of Ty1 transposition protein 102
K: Actin-related protein 7
L: Actin-like protein ARP9


Theoretical massNumber of molelcules
Total (without water)935,47012
Polymers935,47012
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area105490 Å2
ΔGint-630 kcal/mol
Surface area166180 Å2

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Components

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

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


Mass: 63947.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P53628
#3: Protein Transcription regulatory protein SNF6 / SWI/SNF complex component SNF6


Mass: 37652.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P18888
#6: 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: 194315.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
References: UniProt: P22082, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Protein , 6 types, 7 molecules BDEGJKL

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


Mass: 93034.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P32591
#4: Protein SWI/SNF global transcription activator complex subunit SWP82


Mass: 70366.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P43554
#8: Protein Unkown


Mass: 7600.243 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
#9: Protein Regulator of Ty1 transposition protein 102


Mass: 17817.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P53330
#10: Protein Actin-related protein 7 / Actin-like protein ARP7 / Chromatin structure-remodeling complex protein ARP7 / SWI/SNF complex component ARP7


Mass: 53863.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q12406
#11: Protein Actin-like protein ARP9 / Chromatin structure-remodeling complex protein ARP9 / SWI/SNF complex component ARP9


Mass: 53131.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: Q05123

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

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


Mass: 102642.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P18480
#7: 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: 148065.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / References: UniProt: P09547

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Details

Sequence detailsAuthors state that the residues except Ala were basically generated from our EM map and seem like ...Authors state that the residues except Ala were basically generated from our EM map and seem like those side-chains for the chain G (unknown molecule).

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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: the yeast Swi/Snf complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.14 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288C
Buffer solutionpH: 7.4
SpecimenEmbedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 386469 / Symmetry type: POINT
RefinementHighest resolution: 2.89 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00722752
ELECTRON MICROSCOPYf_angle_d0.72930722
ELECTRON MICROSCOPYf_dihedral_angle_d21.8712936
ELECTRON MICROSCOPYf_chiral_restr0.0463455
ELECTRON MICROSCOPYf_plane_restr0.0053933

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