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- EMDB-30630: CHD7 N-CRD and nucleosome(+40bp) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30630
TitleCHD7 N-CRD and nucleosome(+40bp) complex
Map data
Sample
  • Complex: Cryo EM structure of CHD7 N-CRD bound to the nucleosome
    • Complex: CHD7 N-CRD
      • Other: CHD7 N-CRD
    • Complex: Histone
      • Other: Histone H3
      • Other: Histone H4
      • Other: Histone H2A
      • Other: Histone H2B
    • Complex: DNA
      • RNA: widom 601 DNA with extra 40bp of vector sequence
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.14 Å
AuthorsLee E / Song J
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1A2B5B03001517 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2016K1A1A2912057 Korea, Republic Of
CitationJournal: J Mol Biol / Year: 2021
Title: A Novel N-terminal Region to Chromodomain in CHD7 is Required for the Efficient Remodeling Activity.
Authors: Eunhye Lee / Chanshin Kang / Pasi Purhonen / Hans Hebert / Karim Bouazoune / Sungchul Hohng / Ji-Joon Song /
Abstract: Chromodomain-Helicase DNA binding protein 7 (CHD7) is an ATP dependent chromatin remodeler involved in maintaining open chromatin structure. Mutations of CHD7 gene causes multiple developmental ...Chromodomain-Helicase DNA binding protein 7 (CHD7) is an ATP dependent chromatin remodeler involved in maintaining open chromatin structure. Mutations of CHD7 gene causes multiple developmental disorders, notably CHARGE syndrome. However, there is not much known about the molecular mechanism by which CHD7 remodels nucleosomes. Here, we performed biochemical and biophysical analysis on CHD7 chromatin remodeler and uncover that N-terminal to the Chromodomain (N-CRD) interacts with nucleosome and contains a high conserved arginine stretch, which is reminiscent of arginine anchor. Importantly, this region is required for efficient ATPase stimulation and nucleosome remodeling activity of CHD7. Furthermore, smFRET analysis shows the mutations in the N-CRD causes the defects in remodeling activity. Collectively, our results uncover the functional importance of a previously unidentified N-terminal region in CHD7 and implicate that the multiple domains in chromatin remodelers are involved in regulating their activities.
History
DepositionOct 20, 2020-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateMay 4, 2022-
Current statusMay 4, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0063
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0063
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30630.png

Downloads & links

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Map

FileDownload / File: emd_30630.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.144 Å
Density
Contour LevelBy AUTHOR: 0.00627 / Movie #1: 0.0063
Minimum - Maximum-0.022163993 - 0.094645485
Average (Standard dev.)0.00072098855 (±0.0042555155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 228.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1441.1441.144
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z228.800228.800228.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ220220220
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0220.0950.001

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Supplemental data

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Sample components

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Entire : Cryo EM structure of CHD7 N-CRD bound to the nucleosome

EntireName: Cryo EM structure of CHD7 N-CRD bound to the nucleosome
Components
  • Complex: Cryo EM structure of CHD7 N-CRD bound to the nucleosome
    • Complex: CHD7 N-CRD
      • Other: CHD7 N-CRD
    • Complex: Histone
      • Other: Histone H3
      • Other: Histone H4
      • Other: Histone H2A
      • Other: Histone H2B
    • Complex: DNA
      • RNA: widom 601 DNA with extra 40bp of vector sequence

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Supramolecule #1: Cryo EM structure of CHD7 N-CRD bound to the nucleosome

SupramoleculeName: Cryo EM structure of CHD7 N-CRD bound to the nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: CHD7 N-CRD

SupramoleculeName: CHD7 N-CRD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Histone

SupramoleculeName: Histone / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: DNA

SupramoleculeName: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6

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Macromolecule #1: CHD7 N-CRD

MacromoleculeName: CHD7 N-CRD / type: other / ID: 1 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: IEQQPQQKKK KKKNNHIVAE DPSKGFGKDD FPGGVDNQEL NRNSLDGSQE EKKKKKRSKA KKDPKEPKEP KEKKEPKEPK TPKAPKIPKE PKEKKAKTAT PKPKSSKKSS NKKPDSEASA LKKKVNKGKT EGSENSDLDK TPPPSPPPEE DEDPGVQKRR SSRQVKRKRY ...String:
IEQQPQQKKK KKKNNHIVAE DPSKGFGKDD FPGGVDNQEL NRNSLDGSQE EKKKKKRSKA KKDPKEPKEP KEKKEPKEPK TPKAPKIPKE PKEKKAKTAT PKPKSSKKSS NKKPDSEASA LKKKVNKGKT EGSENSDLDK TPPPSPPPEE DEDPGVQKRR SSRQVKRKRY TEDLEFKISD EEADDADAAG RDSPSNTSQS EQQESVDAEG P
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: Histone H3

MacromoleculeName: Histone H3 / type: other / ID: 2 / Classification: other
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAVM ALQEASEAYL VALFEDTNLC AIHAKRVTIM PKDIQLARRI RGERA
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: other / ID: 3 / Classification: other
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #4: Histone H2A

MacromoleculeName: Histone H2A / type: other / ID: 4 / Classification: other
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLPN IQSVLLPKKT ESSKSAKSK
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #5: Histone H2B

MacromoleculeName: Histone H2B / type: other / ID: 5 / Classification: other
Source (natural)Organism: Xenopus laevis (African clawed frog)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSRE IQTAVRLLLP GELAKHAVSE GTKAVTKYTS AK
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #6: widom 601 DNA with extra 40bp of vector sequence

MacromoleculeName: widom 601 DNA with extra 40bp of vector sequence / type: rna / ID: 6
Source (natural)Organism: synthetic construct (others)
SequenceString:
ATCGAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTCC CTAGTCTCCA GGCACGTGTC AGATATATAC ATCCGATTTC GATATGAATT CAATCGAATT CCCGCGGCCG CCATGAT

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 39.54 e/Å2

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1kx5

Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 47550
FSC plot (resolution estimation)

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