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- PDB-7eg6: Snf5 Finger Helix bound to the nucleosome -

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Basic information

Entry
Database: PDB / ID: 7eg6
TitleSnf5 Finger Helix bound to the nucleosome
Components
  • (DNA (235-MER)) x 2
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
  • SWI/SNF chromatin-remodeling complex subunit SNF5
KeywordsDNA BINDING PROTEIN/DNA / Chromatin remodeler complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


carbon catabolite activation of transcription / positive regulation of invasive growth in response to glucose limitation / SWI/SNF complex / nuclear chromosome / double-strand break repair via homologous recombination / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / RNA polymerase II-specific DNA-binding transcription factor binding ...carbon catabolite activation of transcription / positive regulation of invasive growth in response to glucose limitation / SWI/SNF complex / nuclear chromosome / double-strand break repair via homologous recombination / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / RNA polymerase II-specific DNA-binding transcription factor binding / chromatin remodeling / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A ...SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / SWI/SNF chromatin-remodeling complex subunit SNF5 / Histone H4 / Histone H3.2
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: 3.1 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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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-31106
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: SWI/SNF chromatin-remodeling complex subunit SNF5
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (235-MER)
J: DNA (235-MER)


Theoretical massNumber of molelcules
Total (without water)355,87511
Polymers355,87511
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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Protein , 5 types, 9 molecules MAEBFCGDH

#1: 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 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
#2: 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
#3: 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
#4: Protein Histone H2A type 1


Mass: 13978.241 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: P06897
#5: 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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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (235-MER)


Mass: 72380.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (235-MER)


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

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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
1Chromatin remodeler complex SWI/SNF, Snf5 Finger Helix bound to the nucleosomeCOMPLEXall0MULTIPLE SOURCES
2Snf5 Finger HelixCOMPLEX#11RECOMBINANT
3HistoneCOMPLEX#2-#51RECOMBINANT
4DNACOMPLEX#6-#71SYNTHETIC
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 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 525389 / Symmetry type: POINT

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