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- PDB-5o9g: Structure of nucleosome-Chd1 complex -

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Entry
Database: PDB / ID: 5o9g
TitleStructure of nucleosome-Chd1 complex
DescriptorHistone H3.2
Histone H4
Histone H2A
Histone H2B 1.1
Chromo domain-containing protein 1/DNA Complex
KeywordsDNA BINDING PROTEIN / ATPase / Complex / Nucleosome / DNA / Chromatin Remodeling
Specimen sourceXenopus laevis / amphibia / African clawed frog /
Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
Synthetic construct
MethodElectron microscopy (4.8 Å resolution / Particle / Single particle)
AuthorsFarnung, L. / Vos, S.M. / Wigge, C. / Cramer, P.
CitationNature, 2017, 550, 539-542

Nature, 2017, 550, 539-542 Yorodumi Papers
Nucleosome-Chd1 structure and implications for chromatin remodelling.
Lucas Farnung / Seychelle M Vos / Christoph Wigge / Patrick Cramer

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 19, 2017 / Release: Oct 11, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 11, 2017Structure modelrepositoryInitial release
1.1Oct 25, 2017Structure modelDatabase referencescitation_citation.pdbx_database_id_PubMed / _citation.title
1.2Nov 1, 2017Structure modelDatabase referencescitation_citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (162-MER)
J: DNA (162-MER)
W: Chromo domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,48813
Polyers405,99511
Non-polymers4932
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)60910
ΔGint (kcal/M)-382
Surface area (Å2)128510
MethodPISA

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Components

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Polypeptide(L) , 4 types, 7 molecules AEBFCGW

#1: Polypeptide(L)Histone H3.2


Mass: 15435.126 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / References: UniProt: P84233

Cellular component

Molecular function

#2: Polypeptide(L)Histone H4


Mass: 11394.426 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / References: UniProt: P62799

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)Histone H2A


Mass: 14109.436 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis / References: UniProt: Q6AZJ8
#8: Polypeptide(L)Chromo domain-containing protein 1 / ATP-dependent helicase CHD1


Mass: 168496.609 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288c / References: UniProt: P32657, EC: 3.6.4.-

Cellular component

Molecular function

Biological process

  • ATP-dependent chromatin remodeling (GO: 0043044)
  • histone H2B conserved C-terminal lysine ubiquitination (GO: 0071894)
  • negative regulation of DNA-dependent DNA replication (GO: 2000104)
  • negative regulation of histone exchange (GO: 1900050)
  • negative regulation of histone H3-K14 acetylation (GO: 0071441)
  • negative regulation of histone H3-K9 acetylation (GO: 2000616)
  • nucleosome mobilization (GO: 0042766)
  • nucleosome organization (GO: 0034728)
  • nucleosome positioning (GO: 0016584)
  • regulation of chromatin organization (GO: 1902275)
  • regulation of nucleosome density (GO: 0060303)
  • regulation of transcriptional start site selection at RNA polymerase II promoter (GO: 0001178)
  • termination of RNA polymerase I transcription (GO: 0006363)
  • termination of RNA polymerase II transcription (GO: 0006369)
  • transcription elongation from RNA polymerase II promoter (GO: 0006368)

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Histone H2B 1. ... , 2 types, 2 molecules DH

#4: Polypeptide(L)Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 1 / Source: (gene. exp.) Xenopus laevis / References: UniProt: P02281

Cellular component

Molecular function

#5: Polypeptide(L)Histone H2B 1.1 / H2B1.1


Mass: 13526.769 Da / Num. of mol.: 1 / Source: (gene. exp.) Xenopus laevis / References: UniProt: P02281

Cellular component

Molecular function

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chainDNA (162-MER)


Mass: 64143.914 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct
#7: DNA chainDNA (162-MER)


Mass: 64293.945 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct

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Non-polymers , 2 types, 2 molecules

#9: ChemicalChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2
#10: ChemicalChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Formula: BeF3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Protein-Nucleic Acid complexCOMPLEX1, 2, 3, 4, 5, 6, 7, 80MULTIPLE SOURCES
2Protein-Nucleic Acid complexCOMPLEX1, 2, 3, 4, 51RECOMBINANT
3Protein-Nucleic Acid complexCOMPLEX6, 71RECOMBINANT
4Protein-Nucleic Acid complexCOMPLEX81RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
128355Xenopus laevis
3332630synthetic construct
44559292Saccharomyces cerevisiae S288c
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
12562Escherichia coli
247111Trichoplusia ni
3332630synthetic construct
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2750 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / C2 aperture diameter: 150 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 3802
EM imaging opticsEnergyfilter name: GIF Quantum
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategoryImaging IDImage processing ID
2EPUIMAGE ACQUISITION1
4GctfCTF CORRECTION1
13RELION2.0.4RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 990000
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 67032 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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