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- PDB-7egp: The structure of SWI/SNF-nucleosome complex -

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Basic information

Entry
Database: PDB / ID: 7egp
TitleThe structure of SWI/SNF-nucleosome complex
Components
  • (DNA (239-MER)) x 2
  • (SWI/SNF chromatin-remodeling complex subunit ...) x 2
  • (Transcription regulatory protein ...) x 3
  • Actin-like protein ARP9
  • Actin-related protein 7
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • Regulator of Ty1 transposition protein 102
  • 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 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 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via homologous recombination / lysine-acetylated histone binding / DNA-templated DNA replication / chromatin DNA binding / structural constituent of chromatin / double-strand break repair / nucleosome / chromatin organization / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / protein heterodimerization activity / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / structural molecule activity / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / 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 / 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 / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Actin / Actin family / Actin / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / ATPase, nucleotide binding domain / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / helicase superfamily c-terminal domain / Bromodomain / Bromodomain-like superfamily / 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
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / SWI/SNF chromatin-remodeling complex subunit SWI1 / SWI/SNF chromatin-remodeling complex subunit SNF5 / Transcription regulatory protein SNF6 / Transcription regulatory protein SNF2 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / 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 / Histone H4 / Histone H3.2 / Actin-like protein ARP9 / Actin-related protein 7 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Xenopus laevis (African clawed frog)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 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

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Structure visualization

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Assembly

Deposited unit
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
A: Transcription regulatory protein SNF2
L: Regulator of Ty1 transposition protein 102
M: Actin-related protein 7
N: Actin-like protein ARP9
O: Histone H3.2
P: Histone H4
Q: Histone H2A
R: Histone H2B 1.1
S: Histone H3.2
T: Histone H4
U: Histone H2A
V: Histone H2B 1.1
W: DNA (239-MER)
X: DNA (239-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,083,18324
Polymers1,082,66521
Non-polymers5183
Water0
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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SWI/SNF chromatin-remodeling complex subunit ... , 2 types, 2 molecules BC

#1: 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
#2: 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 , 9 types, 14 molecules DEJLMNOSPTQURV

#3: 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
#6: 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
#8: Protein Regulator of Ty1 transposition protein 102


Mass: 17817.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: RTT102, YGR275W, G9378
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P53330
#9: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ARP7, SWP61, YPR034W, YP9367.14
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q12406
#10: 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 genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ARP9, SWP59, YMR033W, YM9973.07
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q05123
#11: Protein Histone H3.2


Mass: 15289.904 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-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P84233
#12: Protein Histone H4 /


Mass: 11263.231 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-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P62799
#13: Protein Histone H2A /


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q6AZJ8
#14: Protein Histone H2B 1.1 / H2B1.1


Mass: 13524.752 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-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P02281

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

#4: 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
#5: 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
#7: 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

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DNA chain , 2 types, 2 molecules WX

#15: DNA chain DNA (239-MER)


Mass: 72380.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#16: DNA chain DNA (239-MER)


Mass: 72740.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 3 molecules

#17: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#18: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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

Component
IDNameTypeEntity IDParent-IDSource
1The structure of SWI/SNF chromatin remodeler complexCOMPLEX#1-#160MULTIPLE SOURCES
2SWI/SNFCOMPLEX#1-#101RECOMBINANT
3HistoneCOMPLEX#11-#141RECOMBINANT
4DNACOMPLEX#15-#161SYNTHETIC
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)559292
23Xenopus laevis (African clawed frog)8355
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)1182032
23Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)1182032
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 FIELDBright-field microscopy
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: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 229461 / Symmetry type: POINT

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