[English] 日本語
Yorodumi
- PDB-6ftx: Structure of the chromatin remodelling enzyme Chd1 bound to a ubi... -

+
Open data


ID or keywords:

Loading...

no data

-
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 H3
  • Histone H4
  • Polyubiquitin-B
KeywordsMOTOR PROTEIN / Chromatin remodellers
Function / homologyChromodomain helicase DNA-binding domain 1 / Pink/Parkin Mediated Mitophagy / CLEC7A (Dectin-1) signaling / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Hedgehog ligand biogenesis / TNFR1-induced NFkappaB signaling pathway / Regulation of TNFR1 signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of FZD by ubiquitination ...Chromodomain helicase DNA-binding domain 1 / Pink/Parkin Mediated Mitophagy / CLEC7A (Dectin-1) signaling / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Hedgehog ligand biogenesis / TNFR1-induced NFkappaB signaling pathway / Regulation of TNFR1 signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of FZD by ubiquitination / Degradation of GLI2 by the proteasome / Degradation of DVL / Degradation of AXIN / Asymmetric localization of PCP proteins / AUF1 (hnRNP D0) binds and destabilizes mRNA / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / activated TAK1 mediates p38 MAPK activation / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / Circadian Clock / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Myoclonic epilepsy of Lafora / Negative regulation of MAPK pathway / UCH proteinases / MAPK6/MAPK4 signaling / HDR through Homologous Recombination (HRR) / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Defective CFTR causes cystic fibrosis / NIK-->noncanonical NF-kB signaling / Regulation of necroptotic cell death / TNFR2 non-canonical NF-kB pathway / Hedgehog 'on' state / Regulation of RAS by GAPs / Termination of translesion DNA synthesis / Translesion synthesis by POLI / Translesion synthesis by POLK / Negative regulation of FGFR4 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR1 signaling / ABC-family proteins mediated transport / Deactivation of the beta-catenin transactivating complex / Ub-specific processing proteases / Vif-mediated degradation of APOBEC3G / p75NTR recruits signalling complexes / NRIF signals cell death from the nucleus / Downstream TCR signaling / TCF dependent signaling in response to WNT / Degradation of beta-catenin by the destruction complex / SCF(Skp2)-mediated degradation of p27/p21 / EGFR downregulation / Vpu mediated degradation of CD4 / Regulation of activated PAK-2p34 by proteasome mediated degradation / APC-Cdc20 mediated degradation of Nek2A / Assembly Of The HIV Virion / Membrane binding and targetting of GAG proteins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Cyclin B / NF-kB is activated and signals survival / NOTCH1 Intracellular Domain Regulates Transcription / Autodegradation of the E3 ubiquitin ligase COP1 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Glycogen synthesis / Regulation of innate immune responses to cytosolic DNA / NOTCH2 Activation and Transmission of Signal to the Nucleus / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Constitutive Signaling by NOTCH1 HD Domain Mutants / Stimuli-sensing channels / Regulation of PLK1 Activity at G2/M Transition / Activated NOTCH1 Transmits Signal to the Nucleus / Oncogene Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Separation of Sister Chromatids / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Downregulation of SMAD2/3:SMAD4 transcriptional activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Ovarian tumor domain proteases / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Amyloid fiber formation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Negative regulation of NOTCH4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex / IRAK1 recruits IKK complex / PRC2 methylates histones and DNA / Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon / Negative regulators of DDX58/IFIH1 signaling / Iron uptake and transport / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of signaling by CBL
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
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 8, 2018Structure modelrepositoryInitial release
1.1Aug 22, 2018Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
1.2Oct 17, 2018Structure modelData collection / Refinement description / Structure summaryem_3d_fitting / entity / refine_em_3d_fitting.target_criteria / _entity.pdbx_description

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4318
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3
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

-
Components

-
Protein/peptide , 7 types, 11 molecules ABFCGDHENOW

#1: Protein/peptide Histone H3 /


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, UniProt: Q28D68*PLUS
#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) / References: UniProt: P32657*PLUS

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
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

-
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 microns / 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

+
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: Cross-correlation coefficient
RefineCorrelation coeff Fo to Fc: 0.304 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 200.492 / Overall SU ML: 0.762 / Overall ESU R: 0.624
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent model details: PARAMETERS FOR MASK CACLULATION
Displacement parametersB iso mean: 266.837 Å2 / Aniso B11: -1.17 Å2 / Aniso B12: 3.67 Å2 / Aniso B13: -0.41 Å2 / Aniso B22: -2.54 Å2 / Aniso B23: 5.45 Å2 / Aniso B33: 3.71 Å2
Least-squares processHighest resolution: 4.5 Å / Percent reflection obs: 1
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

+
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