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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
KeywordsChromatin remodellers / MOTOR PROTEIN
Function / homology
Function and homology information


regulation of transcriptional start site selection at RNA polymerase II promoter / nucleolar chromatin / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / SLIK (SAGA-like) complex / rDNA binding / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / hypothalamus gonadotrophin-releasing hormone neuron development ...regulation of transcriptional start site selection at RNA polymerase II promoter / nucleolar chromatin / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / SLIK (SAGA-like) complex / rDNA binding / DNA double-strand break processing / nucleosome organization / ATP-dependent chromatin remodeler activity / hypothalamus gonadotrophin-releasing hormone neuron development / SAGA complex / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / sister chromatid cohesion / 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 / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / regulation of mitochondrial membrane potential / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL
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 / ATP-dependent helicase CHD1-2/hrp3 HTH domain / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain ...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 / ATP-dependent helicase CHD1-2/hrp3 HTH domain / 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 / Chromo-like domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Homeobox-like domain superfamily / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / helicase superfamily c-terminal domain / 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
Funding support United Kingdom, 1 items
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, 2018-
Header (metadata) releaseAug 8, 2018-
Map releaseAug 8, 2018-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing 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.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 240 pix.
= 336. Å		1.4 Å/pix.
x 240 pix.
= 336. Å		1.4 Å/pix.
x 240 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

Histogram

Histogram (log scale)
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)

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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)

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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)

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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)

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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

UniProtKB: H3.4 histone

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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

UniProtKB: Histone H4

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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

UniProtKB: Histone H2A type 1

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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

UniProtKB: Histone H2B

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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

UniProtKB: Histone H3.3C

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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

UniProtKB: Polyubiquitin-B

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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

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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 mMNaCl
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / 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
TemperatureMin: 170.0 K / Max: 170.0 K
Specialist opticsEnergy filter - Name: GIF Quantum LS
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 - 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
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 FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 35714
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 860000
Startup modelType of model: EMDB MAP
EMDB ID:

3502

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
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
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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