[English] 日本語
Yorodumi
- EMDB-30630: CHD7 N-CRD and nucleosome(+40bp) complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30630
TitleCHD7 N-CRD and nucleosome(+40bp) complex
Map data
SampleCryo EM structure of CHD7 N-CRD bound to the nucleosome:
CHD7 N-CRD / Histone / DNA / (nucleic-acidNucleic acid) x 6
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-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: PDBj / Status: Released

-
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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_30630.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 200 pix.
= 228.8 Å
1.14 Å/pix.
x 200 pix.
= 228.8 Å
1.14 Å/pix.
x 200 pix.
= 228.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

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/NZ-250-250-250
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0220.0950.001

-
Supplemental data

-
Sample components

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

EntireName: Cryo EM structure of CHD7 N-CRD bound to the nucleosome
Number of Components: 10

+
Component #1: protein, Cryo EM structure of CHD7 N-CRD bound to the nucleosome

ProteinName: Cryo EM structure of CHD7 N-CRD bound to the nucleosome
Recombinant expression: No

+
Component #2: protein, CHD7 N-CRD

ProteinName: CHD7 N-CRD / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #3: protein, Histone

ProteinName: Histone / Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #4: protein, DNA

ProteinName: DNA / Recombinant expression: No

+
Component #5: nucleic-acid, CHD7 N-CRD

nucleic acidName: CHD7 N-CRD / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence: IEQQPQQKKK KKKNNHIVAE DPSKGFGKDD FPGGVDNQEL NRNSLDGSQE EKKKKKRSKA KKDPKEPKEP KEKKEPKEPK TPKAPKIPKE PKEKKAKTAT PKPKSSKKSS NKKPDSEASA LKKKVNKGKT EGSENSDLDK TPPPSPPPEE DEDPGVQKRR SSRQVKRKRY ...Sequence:
IEQQPQQKKK KKKNNHIVAE DPSKGFGKDD FPGGVDNQEL NRNSLDGSQE EKKKKKRSKA KKDPKEPKEP KEKKEPKEPK TPKAPKIPKE PKEKKAKTAT PKPKSSKKSS NKKPDSEASA LKKKVNKGKT EGSENSDLDK TPPPSPPPEE DEDPGVQKRR SSRQVKRKRY TEDLEFKISD EEADDADAAG RDSPSNTSQS EQQESVDAEG P
SourceSpecies: Homo sapiens (human)

+
Component #6: nucleic-acid, Histone H3

nucleic acidName: Histone H3 / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAVM ALQEASEAYL VALFEDTNLC AIHAKRVTIM PKDIQLARRI RGERA
SourceSpecies: Xenopus laevis (African clawed frog)

+
Component #7: nucleic-acid, Histone H4

nucleic acidName: Histone H4 / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG
SourceSpecies: Xenopus laevis (African clawed frog)

+
Component #8: nucleic-acid, Histone H2A

nucleic acidName: Histone H2A / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLPN IQSVLLPKKT ESSKSAKSK
SourceSpecies: Xenopus laevis (African clawed frog)

+
Component #9: nucleic-acid, Histone H2B

nucleic acidName: Histone H2B / Class: OTHER / Structure: OTHER / Synthetic: No
Sequence:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSRE IQTAVRLLLP GELAKHAVSE GTKAVTKYTS AK
SourceSpecies: Xenopus laevis (African clawed frog)

+
Component #10: nucleic-acid, widom 601 DNA with extra 40bp of vector sequence

nucleic acidName: widom 601 DNA with extra 40bp of vector sequence / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
ATCGAGAATC CCGGTGCCGA GGCCGCTCAA TTGGTCGTAG ACAGCTCTAG CACCGCTTAA ACGCACGTAC GCGCTGTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTCC CTAGTCTCCA GGCACGTGTC AGATATATAC ATCCGATTTC GATATGAATT CAATCGAATT CCCGCGGCCG CCATGAT
SourceSpecies: synthetic construct (others)

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen Name: ETHANE

-
Electron microscopy imaging

ImagingMicroscope: TFS GLACIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 39.54 e/Å2 / Illumination Mode: OTHER
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 47550
3D reconstructionResolution: 7.14 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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