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

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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 / homology
Function and homology information


Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Packaging Of Telomere Ends / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / Ub-specific processing proteases / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends ...Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Packaging Of Telomere Ends / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / HATs acetylate histones / Ub-specific processing proteases / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Deposition of new CENPA-containing nucleosomes at the centromere / E3 ubiquitin ligases ubiquitinate target proteins / : / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / : / NoRC negatively regulates rRNA expression / : / Transcriptional regulation by small RNAs / : / Assembly of the ORC complex at the origin of replication / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Estrogen-dependent gene expression / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / nucleosome organization / rDNA binding / SLIK (SAGA-like) complex / hypothalamus gonadotrophin-releasing hormone neuron development / SAGA complex / ATP-dependent chromatin remodeler activity / sister chromatid cohesion / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / termination of RNA polymerase II transcription / female gonad development / seminiferous tubule development / termination of RNA polymerase I transcription / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ATP-dependent activity, acting on DNA / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / methylated histone binding / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs
Similarity search - Function
Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / : / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Helicase conserved C-terminal domain / Histone H3 signature 1. / Ubiquitin conserved site / Ubiquitin domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Ubiquitin domain signature. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / helicase superfamily c-terminal domain / Ubiquitin domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H3.3C / Histone H2A type 1 / Polyubiquitin-B / Chromo domain-containing protein 1 ...ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H3.3C / Histone H2A type 1 / Polyubiquitin-B / Chromo domain-containing protein 1 / Histone H4 / Histone H2B / H3.4 histone
Similarity search - Component
Biological speciesPetromyzon marinus (sea lamprey)
Xenopus laevis (African clawed frog)
Xenopus tropicalis (tropical clawed frog)
Homo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsSundaramoorthy, R. / Owen-hughes, T. / Norman, D.G. / Hughes, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
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.
History
DepositionFeb 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2Oct 17, 2018Group: Data collection / Refinement description / Structure summary
Category: em_3d_fitting / entity / refine
Item: _em_3d_fitting.target_criteria / _entity.pdbx_description

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Structure visualization

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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
Polymers320,39213
Non-polymers4932
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area60500 Å2
ΔGint-370 kcal/mol
Surface area142720 Å2
MethodPISA

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Components

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Protein , 7 types, 11 molecules ABFCGDHENOW

#1: Protein Histone H3 /


Mass: 11431.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Escherichia coli (E. coli) / References: UniProt: S4RAZ3
#2: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1


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


Mass: 13939.228 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: LOC108648866 / Production host: Escherichia coli (E. coli) / References: UniProt: F6TNY0, UniProt: Q28D68*PLUS
#5: Protein Histone H3.3C


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


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


Mass: 102152.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CHD1, SCKG_4184 / Production host: Escherichia coli (E. coli) / References: UniProt: P32657*PLUS

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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 method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (160-MER)


Mass: 49678.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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 / Source method: obtained synthetically / Formula: BeF3
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D 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 Chd1COMPLEX#1-#90MULTIPLE SOURCES
2X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1COMPLEX#1-#51RECOMBINANT
3X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1COMPLEX#6-#71RECOMBINANT
4X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1COMPLEX#81RECOMBINANT
5X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1COMPLEX#91RECOMBINANT
Molecular weightValue: 0.450 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Xenopus laevis (African clawed frog)8355
33synthetic construct (others)32630
44Saccharomyces cerevisiae (brewer's yeast)4932
55Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33synthetic construct (others)32630
44Escherichia coli (E. coli)562
55Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMHepes1
2100 mMNaClSodium chloride1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was gel filtration purified and it is monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: 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 X / Calibrated magnification: 35714 X / 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 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 170 K / Temperature (min): 170 K
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) / Num. of grids imaged: 1 / Num. of real images: 1300
EM imaging opticsEnergyfilter name: GIF Quantum LS
Image scansSampling size: 5 µm / 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 selectionNum. of particles selected: 860000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135000 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 204 / Protocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: Cross-correlation coefficient
RefinementCor.coef. Fo:Fc: 0.304 / Highest resolution: 4.5 Å / % reflection obs: 100 % / SU B: 200.492 / SU ML: 0.762 / ESU R: 0.624
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 266.837 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å23.67 Å2-0.41 Å2
2---2.54 Å25.45 Å2
3---3.71 Å2
Refinement stepCycle: 1 / Total: 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_deg19.554152634
ELECTRON MICROSCOPYr_dihedral_angle_4_deg20.54915141
ELECTRON MICROSCOPYr_chiral_restr0.270.2123009
ELECTRON MICROSCOPYr_gen_planes_refined0.0170.0220256
ELECTRON MICROSCOPYr_gen_planes_other0.0060.024240
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_other43.0828.38514924
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
LS refinement shellResolution: 4.5→4.625 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.624 52733 -
obs--100 %

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