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- EMDB-3765: Structure of nucleosome-Chd1 complex -

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Basic information

Entry
Database: EMDB / ID: 3765
TitleStructure of nucleosome-Chd1 complex
Map data
SampleProtein-Nucleic Acid complex:
Histone H3.2 / Histone H4 / Histone H2A / (Histone H2B 1. ...) x 2 / (nucleic-acidNucleic acid) x 2 / Chromo domain-containing protein 1 / (ligand) x 2
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
SourceXenopus laevis (African clawed frog) / synthetic construct (others) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / 4.8 Å resolution
AuthorsFarnung L / Vos SM
CitationJournal: Nature / Year: 2017
Title: Nucleosome-Chd1 structure and implications for chromatin remodelling.
Authors: Lucas Farnung / Seychelle M Vos / Christoph Wigge / Patrick Cramer
Validation ReportPDB-ID: 5o9g

SummaryFull reportAbout validation report
DateDeposition: Jun 19, 2017 / Header (metadata) release: Jul 19, 2017 / Map release: Oct 11, 2017 / Last update: Nov 1, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0317
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0317
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5o9g
  • Surface level: 0.0317
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3765.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.37 Å/pix.
= 328.8 Å
240 pix
1.37 Å/pix.
= 328.8 Å
240 pix
1.37 Å/pix.
= 328.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density
Contour Level:0.0317 (by author), 0.0317 (movie #1):
Minimum - Maximum-0.06631131 - 0.14244908
Average (Standard dev.)0.0005557438 (0.005116877)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin000
Limit239239239
Spacing240240240
CellA=B=C: 328.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z328.800328.800328.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0660.1420.001

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Supplemental data

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Mask #1

Fileemd_3765_msk_1.map ( map file in CCP4 format, 55297 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1

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Mask #1~

Fileemd_3765_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Protein-Nucleic Acid complex

EntireName: Protein-Nucleic Acid complex / Number of components: 14

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Component #1: protein, Protein-Nucleic Acid complex

ProteinName: Protein-Nucleic Acid complex / Recombinant expression: No

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Component #2: protein, Protein-Nucleic Acid complex

ProteinName: Protein-Nucleic Acid complex / Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Protein-Nucleic Acid complex

ProteinName: Protein-Nucleic Acid complex / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, Protein-Nucleic Acid complex

ProteinName: Protein-Nucleic Acid complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #5: protein, Histone H3.2

ProteinName: Histone H3.2 / Recombinant expression: No
MassTheoretical: 15.435126 kDa
Source (engineered)Expression System: Xenopus laevis (African clawed frog)

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Component #6: protein, Histone H4

ProteinName: Histone H4 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
Source (engineered)Expression System: Xenopus laevis (African clawed frog)

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Component #7: protein, Histone H2A

ProteinName: Histone H2A / Recombinant expression: No
MassTheoretical: 14.109436 kDa
Source (engineered)Expression System: Xenopus laevis (African clawed frog)

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Component #8: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Recombinant expression: No
MassTheoretical: 13.655948 kDa
Source (engineered)Expression System: Xenopus laevis (African clawed frog)

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Component #9: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Recombinant expression: No
MassTheoretical: 13.526769 kDa
Source (engineered)Expression System: Xenopus laevis (African clawed frog)

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Component #10: nucleic-acid, DNA (162-MER)

Nucleic-acidName: DNA (162-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DC)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC) (DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC)(DG) (DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DA) (DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC) (DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA) (DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DG)(DA)(DT)(DT)(DA)(DA)(DC)(DG) (DA)(DT)(DG)(DC)(DT)(DG)(DG)(DG)(DC)(DA) (DT)(DA)(DA)(DG)(DC)(DG)(DT)(DG)(DG)(DT) (DT)(DC)(DA)(DA)(DT)(DA)(DC)(DC)(DG)(DG) (DC)(DG)(DC)(DA)(DT)(DA)(DA)(DA)(DG)(DG) (DG)(DT)(DA)(DA)(DA)(DT)(DT)(DC)(DG)(DA) (DA)(DA)(DA)(DC)(DA)(DG)(DC)(DG)
MassTheoretical: 64.143914 kDa

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Component #11: nucleic-acid, DNA (162-MER)

Nucleic-acidName: DNA (162-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DG)(DC)(DT)(DG)(DT)(DT)(DT)(DT)(DC) (DG)(DA)(DA)(DT)(DT)(DT)(DA)(DC)(DC)(DC) (DT)(DT)(DT)(DA)(DT)(DG)(DC)(DG)(DC)(DC) (DG)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DA)(DC) (DC)(DA)(DC)(DG)(DC)(DT)(DT)(DA)(DT)(DG) (DC)(DC)(DC)(DA)(DG)(DC)(DA)(DT)(DC)(DG) (DT)(DT)(DA)(DA)(DT)(DC)(DG)(DA)(DT)(DG) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG) (DA)(DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT) (DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG) (DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT) (DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC) (DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT) (DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT) (DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG) (DA)(DT)(DT)(DC)(DT)(DG)(DA)(DT)
MassTheoretical: 64.293945 kDa

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Component #12: protein, Chromo domain-containing protein 1

ProteinName: Chromo domain-containing protein 1 / Recombinant expression: No
MassTheoretical: 168.496609 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae S288c (yeast)

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Component #13: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #14: ligand, BERYLLIUM TRIFLUORIDE ION

LigandName: BERYLLIUM TRIFLUORIDE ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.600705 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: OTHER
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1250 - 2750 nm / Energy filter: GIF Quantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3802

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 67032
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Output model

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