[English] 日本語
Yorodumi
- EMDB-3502: Structural reorganization of the chromatin remodeling enzyme Chd1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3502
TitleStructural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
Map dataStructure of S.cerevisiae chromatin remodeling enzyme Chd1 bound to Nucleosome.
Sample
  • Complex: Chd1-Nucleosome complex
    • Complex: chd1
    • Complex: nucleosome
    • Other: Chromodomain-Helicase-DNA containing protein
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsSundaramoorthy R / Owen-Hughes T
CitationJournal: Elife / Year: 2017
Title: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.
Authors: Ramasubramanian Sundaramoorthy / Amanda L Hughes / Vijender Singh / Nicola Wiechens / Daniel P Ryan / Hassane El-Mkami / Maxim Petoukhov / Dmitri I Svergun / Barbara Treutlein / Salina Quack ...Authors: Ramasubramanian Sundaramoorthy / Amanda L Hughes / Vijender Singh / Nicola Wiechens / Daniel P Ryan / Hassane El-Mkami / Maxim Petoukhov / Dmitri I Svergun / Barbara Treutlein / Salina Quack / Monika Fischer / Jens Michaelis / Bettina Böttcher / David G Norman / Tom Owen-Hughes /
Abstract: The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding ...The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.
History
DepositionNov 15, 2016-
Header (metadata) releaseDec 14, 2016-
Map releaseApr 5, 2017-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.049
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.049
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_3502.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of S.cerevisiae chromatin remodeling enzyme Chd1 bound to Nucleosome.
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.049 / Movie #1: 0.049
Minimum - Maximum-0.054358844 - 0.20822248
Average (Standard dev.)0.0010571269 (±0.012176228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 335.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z335.000335.000335.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0540.2080.001

-
Supplemental data

-
Half map: Half map1 of the reconstruction

Fileemd_3502_half_map_1.map
AnnotationHalf map1 of the reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: Half map2 of the reconstruction

Fileemd_3502_half_map_2.map
AnnotationHalf map2 of the reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire : Chd1-Nucleosome complex

EntireName: Chd1-Nucleosome complex
Components
  • Complex: Chd1-Nucleosome complex
    • Complex: chd1
    • Complex: nucleosome
    • Other: Chromodomain-Helicase-DNA containing protein

-
Supramolecule #1: Chd1-Nucleosome complex

SupramoleculeName: Chd1-Nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: S.cerevisiae chromatin remodelling enzyme in complex with Nucleosome
Molecular weightTheoretical: 400 KDa

-
Supramolecule #2: chd1

SupramoleculeName: chd1 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Supramolecule #3: nucleosome

SupramoleculeName: nucleosome / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

-
Macromolecule #1: Chromodomain-Helicase-DNA containing protein

MacromoleculeName: Chromodomain-Helicase-DNA containing protein / type: other / ID: 1 / Classification: other
SequenceString: MAAKDISTEV LQNPELYGLR RSHRAAAHQQ NYFNDSDDED DEDNIKQSRR KRMTTIEDDE DEFEDEEGE EDSGEDEDEE DFEEDDDYYG SPIKQNRSKP KSRTKSKSKS KPKSQSEKQS T VKIPTRFS NRQNKTVNYN IDYSDDDLLE SEDDYGSEEA LSEENVHEAS ...String:
MAAKDISTEV LQNPELYGLR RSHRAAAHQQ NYFNDSDDED DEDNIKQSRR KRMTTIEDDE DEFEDEEGE EDSGEDEDEE DFEEDDDYYG SPIKQNRSKP KSRTKSKSKS KPKSQSEKQS T VKIPTRFS NRQNKTVNYN IDYSDDDLLE SEDDYGSEEA LSEENVHEAS ANPQPEDFHG ID IVINHRL KTSLEEGKVL EKTVPDLNNC KENYEFLIKW TDESHLHNTW ETYESIGQVR GLK RLDNYC KQFIIEDQQV RLDPYVTAED IEIMDMERER RLDEFEEFHV PERIIDSQRA SLED GTSQL QYLVKWRRLN YDEATWENAT DIVKLAPEQV KHFQNRENSK ILPQYSSNYT SQRPR FEKL SVQPPFIKGG ELRDFQLTGI NWMAFLWSKG DNGILADEMG LGKTVQTVAF ISWLIF ARR QNGPHIIVVP LSTMPAWLDT FEKWAPDLNC ICYMGNQKSR DTIREYEFYT NPRAKGK KT MKFNVLLTTY EYILKDRAEL GSIKWQFMAV DEAHRLKNAE SSLYESLNSF KVANRMLI T GTPLQNNIKE LAALVNFLMP GRFTIDQEID FENQDEEQEE YIHDLHRRIQ PFILRRLKK DVEKSLPSKT ERILRVELSD VQTEYYKNIL TKNYSALTAG AKGGHFSLLN IMNELKKASN HPYLFDNAE ERVLQKFGDG KMTRENVLRG LIMSSGKMVL LDQLLTRLKK DGHRVLIFSQ M VRMLDILG DYLSIKGINF QRLDGTVPSA QRRISIDHFN SPDSNDFVFL LSTRAGGLGI NL MTADTVV IFDSDWNPQA DLQAMARAHR IGQKNHVMVY RLVSKDTVEE EVLERARKKM ILE YAIISL GVTDGNKYTK KNEPNAGELS AILKFGAGNM FTATDNQKKL EDLNLDDVLN HAED HVTTP DLGESHLGGE EFLKQFEVTD YKADIDWDDI IPEEELKKLQ DEEQKRKDEE YVKEQ LEMM NRRDNALKKI KNSVNGDGTA ANSDSDDDST SRSSRRRARA NDMDSIGESE VRALYK AIL KFGNLKEILD ELIADGTLPV KSFEKYGETY DEMMEAAKDC VHEEEKNRKE ILEKLEK HA TAYRAKLKSG EIKAENQPKD NPLTRLSLKK REKKAVLFNF KGVKSLNAES LLSRVEDL K YLKNLINSNY KDDPLKFSLG NNTPKPVQNW SSNWTKEEDE KLLIGVFKYG YGSWTQIRD DPFLGITDKI FLNEVHNPVA KKSASSSDTT PTPSKKGKGI TGSSKKVPGA IHLGRRVDYL LSFLRGGLN TKSPSADIGS KKLPTGPSKK RQRKPANHSK SMTPEI

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMTristris(hydroxymethyl)aminomethane
50.0 mMNaClSodium chlorideSodium Chloride

Details: Solutions were made fresh
GridModel: Quantifoil / Material: COPPER/RHODIUM / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100.00 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse. One Chd1 enzyme bound to the Nucleosome

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.8 µm / Calibrated magnification: 59000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 4-18 / Number grids imaged: 1 / Number real images: 2560 / Average exposure time: 1.0 sec. / Average electron dose: 2.27 e/Å2
Details: Images are collected in movie mode at 22 images per second
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 280000
Details: Particles are picked using RELION 1.4 autopick routine
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

Details: Nucleosome structure 1KX5 was converted into map of pixel size 1.34, low pass filtered and used as a initial model
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 2 / Avg.num./class: 26000
Final angle assignmentType: PROJECTION MATCHING / Projection matching processing - Merit function: CC
Projection matching processing - Angular sampling: 3.5 degrees
Software - Name: RELION (ver. 1.4)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Details: RELION 1.4 was used for the reconstruction. / Number images used: 52208
DetailsThe selected images were high pass filtered and framwise movie corrected for drift.
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

chain_id: A, B, C, D, E, F, G, H, I, J

chain_id: A, residue_range: 175-932

chain_id: A, B, C, residue_range: 1010-1274
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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