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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 / homologyRegulation of PLK1 Activity at G2/M Transition / TNFR2 non-canonical NF-kB pathway / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling ...Regulation of PLK1 Activity at G2/M Transition / TNFR2 non-canonical NF-kB pathway / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / 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 / Negative regulation of MAPK pathway / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Regulation of necroptotic cell death / NIK-->noncanonical NF-kB signaling / Defective CFTR causes cystic fibrosis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / MAPK6/MAPK4 signaling / UCH proteinases / Josephin domain DUBs / Ub-specific processing proteases / Ovarian tumor domain proteases / Metalloprotease DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / DNA Damage Recognition in GG-NER / Dectin-1 mediated noncanonical NF-kB signaling / Hedgehog ligand biogenesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Autodegradation of the E3 ubiquitin ligase COP1 / 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 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Stimuli-sensing channels / Constitutive Signaling by NOTCH1 HD Domain Mutants / 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 / Deactivation of the beta-catenin transactivating complex / TNFR1-induced NFkappaB signaling pathway / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Asymmetric localization of PCP proteins / Degradation of AXIN / 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 / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Ub-specific processing proteases / TRAF6-mediated induction of TAK1 complex within TLR4 complex / NOTCH3 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / TICAM1,TRAF6-dependent induction of TAK1 complex / 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 / Negative regulation of NOTCH4 signaling / ER Quality Control Compartment (ERQC) / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Amyloid fiber formation / Antigen processing: Ubiquitination & Proteasome degradation / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / HDACs deacetylate histones / HATs acetylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Transcriptional regulation by small RNAs / Regulation of expression of SLITs and ROBOs / Neddylation
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
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  • 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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