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- EMDB-4318: Structure of the chromatin remodelling enzyme Chd1 bound to a ubi... -

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Entry
Database: EMDB / ID: 4318
TitleStructure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome
Map dataCryoEM reconstruction for a S.cerevisiae chromatin remodeller bound to 601 nucleosome.
SampleX. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1:
Histone H3 / Histone H4 / Histone H2A type 1 / Histone H2B / Histone H3.3C / (nucleic-acidNucleic acid) x 2 / Polyubiquitin-B / Chromatin-remodeling ATPase / (ligand) x 2
Function / homologyAutodegradation of Cdh1 by Cdh1:APC/C / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / ISG15 antiviral mechanism / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / ER-Phagosome pathway / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling ...Autodegradation of Cdh1 by Cdh1:APC/C / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / ISG15 antiviral mechanism / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / ER-Phagosome pathway / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / Budding and maturation of HIV virion / NOD1/2 Signaling Pathway / TICAM1, RIP1-mediated IKK complex recruitment / APC/C:Cdc20 mediated degradation of Cyclin B / Translesion synthesis by REV1 / MAPK6/MAPK4 signaling / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Membrane binding and targetting of GAG proteins / Assembly Of The HIV Virion / APC-Cdc20 mediated degradation of Nek2A / Vpu mediated degradation of CD4 / Vif-mediated degradation of APOBEC3G / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / Recognition of DNA damage by PCNA-containing replication complex / Superfamilies 1 and 2 helicase C-terminal domain profile. / Downstream TCR signaling / Ubiquitin family / Chromo domain, conserved site / Chromo domain / Domain of unknown function DUF4208 / P-loop containing nucleoside triphosphate hydrolase / Ubiquitin-like domain superfamily / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / Chromo domain-containing protein 1 / SNF2-like, N-terminal domain superfamily / Core histone H2A/H2B/H3/H4 / SNF2 family N-terminal domain / Helicase conserved C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Chromo (CHRromatin Organisation MOdifier) domain / Domain of unknown function (DUF4208) / Centromere kinetochore component CENP-T histone fold / C-terminus of histone H2A / Histone H2A signature. / Histone H4 signature. / Ubiquitin domain signature. / Histone H3 signature 1. / Histone H2B signature. / Chromo domain signature. / Histone H3 signature 2. / Chromo and chromo shadow domain profile. / Ubiquitin domain profile. / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / Ubiquitin conserved site / GLI3 is processed to GLI3R by the proteasome / Degradation of DVL / Regulation of FZD by ubiquitination / Pink/Parkin Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NFkappaB signaling pathway / Hedgehog ligand biogenesis / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / Hedgehog 'on' state / Asymmetric localization of PCP proteins / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / Regulation of RAS by GAPs / TNFR2 non-canonical NF-kB pathway / Negative regulation of MAPK pathway / Regulation of necroptotic cell death / NIK-->noncanonical NF-kB signaling / Defective CFTR causes cystic fibrosis / Degradation of AXIN / AUF1 (hnRNP D0) binds and destabilizes mRNA / p75NTR recruits signalling complexes / Constitutive Signaling by NOTCH1 PEST Domain Mutants / NF-kB is activated and signals survival / Regulation of activated PAK-2p34 by proteasome mediated degradation / NOTCH1 Intracellular Domain Regulates Transcription / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling
Function and homology information
SourceXenopus laevis (African clawed frog) / synthetic construct (others) / Saccharomyces cerevisiae (baker's yeast) / Homo sapiens (human) / Petromyzon marinus (sea lamprey) / Xenopus tropicalis (tropical clawed frog)
Methodsingle particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsSundaramoorthy R / Owen-hughes T / Norman DG / Hughes A
CitationJournal: Elife / Year: 2018
Title: Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome.
Authors: Ramasubramanian Sundaramoorthy / Amanda L Hughes / Hassane El-Mkami / David G Norman / Helder Ferreira / Tom Owen-Hughes
Abstract: ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the ...ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.
Validation ReportPDB-ID: 6ftx

SummaryFull reportAbout validation report
DateDeposition: Feb 25, 2018 / Header (metadata) release: Aug 8, 2018 / Map release: Aug 8, 2018 / Last update: Oct 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6ftx
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4318.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
1.4 Å/pix.
= 336. Å
240 pix
1.4 Å/pix.
= 336. Å
240 pix
1.4 Å/pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour Level:0.011 (by author), 0.011 (movie #1):
Minimum - Maximum-0.041239962 - 0.11787542
Average (Standard dev.)0.00020261812 (0.0036416887)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin0.00.00.0
Limit239.0239.0239.0
Spacing240240240
CellA=B=C: 336.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0410.1180.000

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Supplemental data

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Sample components

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Entire X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1

EntireName: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
Number of components: 16

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Component #1: protein, X. laevis nucleosome pn 601 DNA with S.cerevisiae remode...

ProteinName: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
Recombinant expression: No
MassTheoretical: 450 kDa

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Component #2: protein, X. laevis nucleosome pn 601 DNA with S.cerevisiae remode...

ProteinName: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, X. laevis nucleosome pn 601 DNA with S.cerevisiae remode...

ProteinName: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, X. laevis nucleosome pn 601 DNA with S.cerevisiae remode...

ProteinName: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, X. laevis nucleosome pn 601 DNA with S.cerevisiae remode...

ProteinName: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Histone H3

ProteinName: Histone H3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.431358 kDa
SourceSpecies: Petromyzon marinus (sea lamprey)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Histone H2A type 1

ProteinName: Histone H2A type 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.093436 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: protein, Histone H2B

ProteinName: Histone H2B / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.939228 kDa
SourceSpecies: Xenopus tropicalis (tropical clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #10: protein, Histone H3.3C

ProteinName: Histone H3.3C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.32933 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: nucleic-acid, DNA (159-MER)

Nucleic-acidName: DNA (159-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DA)(DC)(DG)(DC)(DG)(DG)(DC)(DC) (DG)(DC)(DC)(DC)(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)
MassTheoretical: 48.792086 kDa
SourceSpecies: synthetic construct (others)

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Component #12: nucleic-acid, DNA (160-MER)

Nucleic-acidName: DNA (160-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(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)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DG)(DA)(DT)(DG)(DG)(DG)(DC) (DG)(DG)(DC)(DC)(DG)(DC)(DG)(DT)(DA)(DT)
MassTheoretical: 49.678613 kDa
SourceSpecies: synthetic construct (others)

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Component #13: protein, Polyubiquitin-B

ProteinName: Polyubiquitin-B / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.576831 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #14: protein, Chromatin-remodeling ATPase

ProteinName: Chromatin-remodeling ATPase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 102.152859 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #15: ligand, BERYLLIUM TRIFLUORIDE ION

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

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Component #16: ligand, ADENOSINE-5'-DIPHOSPHATE

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

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK III / 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: 1.25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 35714.0 X (nominal), 35714.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 4000.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 170.0 - 170.0 K)
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1300 / Sampling size: 5 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 135000
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Cross-correlation coefficient / Refinement space: RECIPROCAL / Overall bvalue: 204
Output model

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