[English] 日本語
Yorodumi
- EMDB-4318: Structure of the chromatin remodelling enzyme Chd1 bound to a ubi... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

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:
Uncharacterized protein / 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 / homologyTGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Hedgehog 'on' state / 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 ...TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Hedgehog 'on' state / 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 / GLI3 is processed to GLI3R by the proteasome / Negative regulation of FGFR1 signaling / Degradation of AXIN / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Degradation of DVL / Asymmetric localization of PCP proteins / MAPK6/MAPK4 signaling / Stimuli-sensing channels / 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 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Separation of Sister Chromatids / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Regulation of PLK1 Activity at G2/M Transition / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / AUF1 (hnRNP D0) binds and destabilizes mRNA / FCERI mediated NF-kB activation / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of innate immune responses to cytosolic DNA / Glycogen synthesis / Autodegradation of the E3 ubiquitin ligase COP1 / Deactivation of the beta-catenin transactivating complex / Myoclonic epilepsy of Lafora / ABC-family proteins mediated transport / Circadian Clock / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / HDR through Homologous Recombination (HRR) / UCH proteinases / NRIF signals cell death from the nucleus / TICAM1-dependent activation of IRF3/IRF7 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / InlB-mediated entry of Listeria monocytogenes into host cell / InlA-mediated entry of Listeria monocytogenes into host cells / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / Regulation of PTEN localization / Regulation of PTEN stability and activity / Neddylation / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / NOTCH3 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / Clathrin-mediated endocytosis / Interleukin-1 signaling / Peroxisomal protein import / Regulation of signaling by CBL / Endosomal Sorting Complex Required For Transport (ESCRT) / Iron uptake and transport / Negative regulators of DDX58/IFIH1 signaling / Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon / IRAK1 recruits IKK complex / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB2 signaling / Cargo recognition for clathrin-mediated endocytosis / Josephin domain DUBs / Fanconi Anemia Pathway / Ub-specific processing proteases / Ovarian tumor domain proteases / Metalloprotease DUBs
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: Aug 8, 2018

-
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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
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
Origin0.0.0.
Limit239.239.239.
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/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0410.1180.000

-
Supplemental data

-
Sample components

+
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

+
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

+
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)

+
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)

+
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)

+
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)

+
Component #6: protein, Uncharacterized protein

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

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
Component #15: ligand, BERYLLIUM TRIFLUORIDE ION

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

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

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

-
Experimental details

-
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 %

-
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. X (nominal), 35714. 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)

-
Image acquisition

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

-
Image processing

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

-
Atomic model buiding

Modeling #1Target criteria: Correlation Coefficient / Refinement space: RECIPROCAL / Overall bvalue: 204
Output model

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more