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

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Basic information

Entry
Database: PDB / ID: 5o9g
TitleStructure of nucleosome-Chd1 complex
Components
  • (DNA (162-MER)) x 2
  • (Histone H2B 1. ...) x 2
  • Chromo domain-containing protein 1
  • Histone H2A
  • Histone H3.2
  • Histone H4
KeywordsDNA BINDING PROTEIN / ATPase / Complex / Nucleosome / DNA / Chromatin Remodeling
Function / homologyHistone H4 / Histone-fold / Histone H3/CENP-A / SNF2-related, N-terminal domain / Histone H2B / Chromo/chromo shadow domain / Helicase, C-terminal / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 ...Histone H4 / Histone-fold / Histone H3/CENP-A / SNF2-related, N-terminal domain / Histone H2B / Chromo/chromo shadow domain / Helicase, C-terminal / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Homeobox-like domain superfamily / Helicase superfamily 1/2, ATP-binding domain / Core histone H2A/H2B/H3/H4 / Chromo-like domain superfamily / Histone H4, conserved site / Chromo domain, conserved site / Chromo domain / Domain of unknown function DUF4208 / P-loop containing nucleoside triphosphate hydrolase / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / SNF2-like, N-terminal domain superfamily / Chromo domain-containing protein 1 / SNF2 family N-terminal domain / Domain of unknown function (DUF4208) / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Chromo and chromo shadow domain profile. / Histone H3 signature 2. / Chromo domain signature. / Histone H2B signature. / Histone H3 signature 1. / Histone H4 signature. / Helicase conserved C-terminal domain / Histone H2A signature. / Chromo (CHRromatin Organisation MOdifier) domain / C-terminus of histone H2A / Centromere kinetochore component CENP-T histone fold / histone H2B conserved C-terminal lysine ubiquitination / nucleosome-dependent ATPase activity / nucleolar chromatin / negative regulation of histone exchange / negative regulation of DNA-dependent DNA replication / regulation of chromatin organization / negative regulation of histone H3-K14 acetylation / regulation of transcriptional start site selection at RNA polymerase II promoter / SLIK (SAGA-like) complex / nucleosome mobilization / regulation of nucleosome density / nucleosome organization / negative regulation of histone H3-K9 acetylation / SAGA complex / nucleosome positioning / rDNA binding / termination of RNA polymerase I transcription / ATP-dependent chromatin remodeling / ec:3.6.4.-: / termination of RNA polymerase II transcription / DNA-dependent ATPase activity / transcription elongation from RNA polymerase II promoter / DNA-templated transcription, initiation / chromatin DNA binding / methylated histone binding / helicase activity / nucleosome / nucleosome assembly / transcription regulatory region DNA binding / nuclear chromatin / protein heterodimerization activity / DNA binding / nucleoplasm / ATP binding / nucleus / Histone H2B 1.1 / Histone H2A type 1 / Chromo domain-containing protein 1 / Histone H4 / Histone H3.2 / Histone H2A
Function and homology information
Specimen sourceXenopus laevis (African clawed frog)
Saccharomyces cerevisiae S288c (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.8 Å resolution
AuthorsFarnung, L. / Vos, S.M. / Wigge, C. / Cramer, P.
CitationJournal: Nature / Year: 2017
Title: Nucleosome-Chd1 structure and implications for chromatin remodelling.
Authors: 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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Structure visualization

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Structure viewerMolecule:
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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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Protein/peptide , 4 types, 7 molecules AEBFCGW

#1: Protein/peptide Histone H3.2


Mass: 15435.126 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein/peptide Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein/peptide Histone H2A /


Mass: 14109.436 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#8: Protein/peptide Chromo domain-containing protein 1 / ATP-dependent helicase CHD1


Mass: 168496.609 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: CHD1, YER164W, SYGP-ORF4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32657, EC: 3.6.4.-

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

#4: Protein/peptide Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 1 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281
#5: Protein/peptide Histone H2B 1.1 / H2B1.1


Mass: 13526.769 Da / Num. of mol.: 1 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (162-MER)


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


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

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Non-polymers , 2 types, 2 molecules

#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#10: Chemical ChemComp-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 reconstruction

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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 (African clawed frog)
3332630synthetic construct (others)
44559292Saccharomyces cerevisiae S288c (yeast)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
12562Escherichia coli (E. coli)
247111Trichoplusia ni (cabbage looper)
3332630synthetic construct (others)
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 FIELDBright-field microscopy / 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
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
13RELION2.0.43D reconstruction
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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