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- PDB-6ftx: Structure of the chromatin remodelling enzyme Chd1 bound to a ubi... -

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Basic information

Entry
Database: PDB / ID: 6ftx
TitleStructure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome
Components
  • Chromatin-remodeling ATPase
  • DNA (159-MER)
  • DNA (160-MER)
  • Histone H2A type 1
  • Histone H2B
  • Histone H3.3C
  • Histone H4
  • Polyubiquitin-B
  • Uncharacterized protein
KeywordsMOTOR PROTEIN / Chromatin remodellers
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
Specimen sourcePetromyzon marinus (sea lamprey)
Xenopus laevis (African clawed frog)
Xenopus tropicalis (tropical clawed frog)
Homo sapiens (human)
Saccharomyces cerevisiae (baker's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 Å resolution
AuthorsSundaramoorthy, R. / Owen-hughes, T. / Norman, D.G. / 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 Report
SummaryFull reportAbout validation report
DateDeposition: Feb 25, 2018 / Release: Aug 8, 2018

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Uncharacterized protein
B: Histone H4
C: Histone H2A type 1
D: Histone H2B
E: Histone H3.3C
F: Histone H4
G: Histone H2A type 1
H: Histone H2B
I: DNA (159-MER)
J: DNA (160-MER)
N: Polyubiquitin-B
O: Polyubiquitin-B
W: Chromatin-remodeling ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,88515
Polyers320,39213
Non-polymers4932
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)60500
ΔGint (kcal/M)-370
Surface area (Å2)142720
MethodPISA

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Components

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Protein/peptide , 7 types, 11 molecules ABFCGDHENOW

#1: Protein/peptide Uncharacterized protein


Mass: 11431.358 Da / Num. of mol.: 1 / Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Escherichia coli (E. coli) / References: UniProt: S4RAZ3
#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 type 1


Mass: 14093.436 Da / Num. of mol.: 2 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein/peptide Histone H2B /


Mass: 13939.228 Da / Num. of mol.: 2
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: LOC108648866 / Production host: Escherichia coli (E. coli) / References: UniProt: F6TNY0
#5: Protein/peptide Histone H3.3C


Mass: 12329.330 Da / Num. of mol.: 1 / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: h3f3c / Production host: Escherichia coli (E. coli) / References: UniProt: P02302
#8: Protein/peptide Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#9: Protein/peptide Chromatin-remodeling ATPase


Mass: 102152.859 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: CHD1, SCKG_4184 / Production host: Escherichia coli (E. coli)

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (159-MER)


Mass: 48792.086 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (160-MER)


Mass: 49678.613 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 2 molecules

#10: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Formula: BeF3
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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

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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
1X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1COMPLEX1,2,3,4,5,6,7,8,90MULTIPLE SOURCES
2X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1COMPLEX1,2,3,4,51RECOMBINANT
3X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1COMPLEX6,71RECOMBINANT
4X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1COMPLEX81RECOMBINANT
5X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1COMPLEX91RECOMBINANT
Molecular weightValue: 0.450 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
228355Xenopus laevis (African clawed frog)
3332630synthetic construct (others)
444932Saccharomyces cerevisiae (baker's yeast)
559606Homo sapiens (human)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
22562Escherichia coli (E. coli)
3332630synthetic construct (others)
44562Escherichia coli (E. coli)
55562Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer ID
120 mMHepes1
2100 mMNaCl1
SpecimenConc.: 1 mg/ml
Details: Sample was gel filtration purified and it is monodisperse
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK III / 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 35714 / Calibrated magnification: 35714 / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 4000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 170 kelvins / Temperature (min): 170 kelvins
Image recordingAverage exposure time: 0.32 sec. / Electron dose: 1.25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1 / Number of real images: 1300
EM imaging opticsEnergyfilter name: GIF Quantum LS
Image scansSampling size: 5 microns / Width: 3870 / Height: 3870 / Movie frames/image: 32 / Used frames/image: 5-28

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Processing

SoftwareName: REFMAC / Version: 5.8.0230 / Classification: refinement
EM software
IDNameCategory
2EPUimage acquisition
4GctfCTF correction
7CCP4 packagemodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 860000
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 135000 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingOverall b value: 204 / Ref protocol: FLEXIBLE FIT / Ref space: RECIPROCAL / Target criteria: Correlation Coefficient
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcDetailsHighest resolutionPercent reflection obsOverall SU BOverall SU MLOverall ESU RStereochemistry target valuesSolvent model details
1266.837-1.173.67-0.41-2.545.453.710.304HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS4.50100.00200.4920.7620.624MAXIMUM LIKELIHOOD WITH PHASESPARAMETERS FOR MASK CACLULATION
ELECTRON MICROSCOPY
Number of atoms included #1Total: 21021
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0280.01322146
ELECTRON MICROSCOPYr_bond_other_d0.0050.01817259
ELECTRON MICROSCOPYr_angle_refined_deg2.3581.48731140
ELECTRON MICROSCOPYr_angle_other_deg1.4721.92140568
ELECTRON MICROSCOPYr_dihedral_angle_1_deg22.2615.7963573
ELECTRON MICROSCOPYr_dihedral_angle_2_deg32.72920.756794
ELECTRON MICROSCOPYr_dihedral_angle_3_deg19.55415.0002634
ELECTRON MICROSCOPYr_dihedral_angle_4_deg20.54915.000141
ELECTRON MICROSCOPYr_chiral_restr0.2700.2123009
ELECTRON MICROSCOPYr_gen_planes_refined0.0170.02020256
ELECTRON MICROSCOPYr_gen_planes_other0.0060.0204240
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it37.44126.0697220
ELECTRON MICROSCOPYr_mcbond_other37.44426.0677219
ELECTRON MICROSCOPYr_mcangle_it60.14838.8948998
ELECTRON MICROSCOPYr_mcangle_other60.14538.8978999
ELECTRON MICROSCOPYr_scbond_it43.07728.38714926
ELECTRON MICROSCOPYr_scbond_other43.08028.38514924
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other67.23442.25922140
ELECTRON MICROSCOPYr_long_range_B_refined104348
ELECTRON MICROSCOPYr_long_range_B_other104337
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 4.5 Å / R factor R free: 0 / R factor R work: 0.624 / Lowest resolution: 4.625 Å / Number reflection R free: 0 / Number reflection R work: 52733 / Total number of bins used: 20 / Percent reflection obs: 1

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