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- EMDB-4318: Structure of the chromatin remodelling enzyme Chd1 bound to a ubi... -

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Basic information

Entry
Database: EMDB / ID: EMD-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.
Sample
  • Complex: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
    • Complex: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
      • Protein or peptide: x 5 types
    • Complex: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
      • DNA: x 2 types
    • Complex: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
      • Protein or peptide: x 1 types
    • Complex: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
      • Protein or peptide: x 1 types
  • Ligand: x 2 types
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 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of FZD by ubiquitination / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / 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
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 speciesXenopus laevis (African clawed frog) / synthetic construct (others) / Saccharomyces cerevisiae (brewer's yeast) / Homo sapiens (human) / Petromyzon marinus (sea lamprey) / Xenopus tropicalis (tropical clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
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.
History
DepositionFeb 25, 2018-
Header (metadata) releaseAug 8, 2018-
Map releaseAug 8, 2018-
UpdateOct 17, 2018-
Current statusOct 17, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • 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

emd_4318.png

Downloads & links

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Map

FileDownload / File: emd_4318.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction for a S.cerevisiae chromatin remodeller bound to 601 nucleosome.
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.011 / Movie #1: 0.011
Minimum - Maximum-0.041239962 - 0.11787542
Average (Standard dev.)0.00020261812 (±0.0036416887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

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
Components
  • Complex: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
    • Complex: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B
      • Protein or peptide: Histone H3.3C
    • Complex: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
      • DNA: DNA (159-MER)
      • DNA: DNA (160-MER)
    • Complex: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
      • Protein or peptide: Polyubiquitin-B
    • Complex: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
      • Protein or peptide: Chromatin-remodeling ATPase
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1

SupramoleculeName: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Molecular weightTheoretical: 450 KDa

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Supramolecule #2: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1

SupramoleculeName: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1

SupramoleculeName: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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Supramolecule #4: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1

SupramoleculeName: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #5: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1

SupramoleculeName: X. laevis nucleosome pn 601 DNA with S.cerevisiae remodeller Chd1
type: complex / ID: 5 / Parent: 1 / Macromolecule list: #9
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Petromyzon marinus (sea lamprey)
Molecular weightTheoretical: 11.431358 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQSS AVMALQEASE AYLVALFEDT NLCAIHAKRV TIMPKDIQL ARRIRGER

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.093436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESAKSAKS K

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Molecular weightTheoretical: 13.939228 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPDPAKSAPA AKKGSKKAVT KTQKKDGKKR RKTRKESYAI YVYKVLKQVH PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

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Macromolecule #5: Histone H3.3C

MacromoleculeName: Histone H3.3C / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 12.32933 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AAAAAAAAAA AAAHRYRPGT VALREIRRYQ KSTELLIRKL PFQRLVREIA QDFKTDLRFQ SSAVMALQEA SEAYLVALFE DTNLCAIHA KRVTIMPKDI QLARRIRGER A

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Macromolecule #8: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

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Macromolecule #9: Chromatin-remodeling ATPase

MacromoleculeName: Chromatin-remodeling ATPase / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 102.152859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DFHGIDIVIN HRLKTSKTVP DLNNCKENYE FLIKWTDESH LHNTWETYES IGQVRGLKRL DNYCKQFIIE DQQVRLDPYV TAEDIEIMD MERERRLDEF EEFHVPERII DSQRASLEDG TSQLQYLVKW RRLNYDEATW ENATDIVKLA PEQVKHFQNR E NSKILPQY ...String:
DFHGIDIVIN HRLKTSKTVP DLNNCKENYE FLIKWTDESH LHNTWETYES IGQVRGLKRL DNYCKQFIIE DQQVRLDPYV TAEDIEIMD MERERRLDEF EEFHVPERII DSQRASLEDG TSQLQYLVKW RRLNYDEATW ENATDIVKLA PEQVKHFQNR E NSKILPQY SSNYTSQRPR FEKLSVQPPF IKGGELRDFQ LTGINWMAFL WSKGDNGILA DEMGLGKTVQ TVAFISWLIF AR RQNGPHI IVVPLSTMPA WLDTFEKWAP DLNCICYMGN QKSRDTIREY EFYTNPRAKG KKTMKFNVLL TTYEYILKDR AEL GSIKWQ FMAVDEAHRL KNAESSLYES LNSFKVANRM LITGTPLQNN IKELAALVNF LMPGRFNQDE EQEEYIHDLH RRIQ PFILR RLKKDVEKSL PSKTERILRV ELSDVQTEYY KNILTKNYSA LTAGAKGGHF SLLNIMNELK KASNHPYLFD NAEER VLQK FMTRENVLRG LIMSSGKMVL LDQLLTRLKK DGHRVLIFSQ MVRMLDILGD YLSIKGINFQ RLDGTVPSAQ RRISID HFN SPDSNDFVFL LSTRAGGLGI NLMTADTVVI FDSDWNPQAD LQAMARAHRI GQKNHVMVYR LVSKDTVEEE VLERARK KM ILEYDMDSIG ESEVRALYKA ILKFGNLKEI LDELIADGTL PVKSFEKYGE TYDEMMEAAK DCVHEEEKNR KEILEKLE K HATAYRAKLK SGEIKAENQP KDNPLTRLSL KKREKKAVLF NFKGVKSLNA ESLLSRVEDL KYLKNLINSN YKDDPLKFS LGNNTPKPVQ NWSSNWTKEE DEKLLIGVFK YGYGSWTQIR DDPFLGITDK IFLKKVPGAI HLGRRVDYLL SFLRGGLN

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Macromolecule #6: DNA (159-MER)

MacromoleculeName: DNA (159-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 48.792086 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #7: DNA (160-MER)

MacromoleculeName: DNA (160-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 49.678613 KDa
SequenceString: (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) ...String:
(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)

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Macromolecule #10: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #11: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHepes
100.0 mMNaClSodium chloride
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III
DetailsSample was gel filtration purified and it is monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 35714
Specialist opticsEnergy filter - Name: GIF Quantum LS
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 170.0 K / Max: 170.0 K
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3870 pixel / Digitization - Dimensions - Height: 3870 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 5-28 / Number grids imaged: 1 / Number real images: 1300 / Average exposure time: 0.32 sec. / Average electron dose: 1.25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 860000
CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

3502

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 135000
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 204 / Target criteria: Cross-correlation coefficient
Output model

PDB-6ftx:
Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

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