[English] 日本語
Yorodumi
- EMDB-1286: An expanded conformation of single-ring GroEL-GroES complex encap... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1286
TitleAn expanded conformation of single-ring GroEL-GroES complex encapsulates an 86 kDa substrate.
Map dataThis is the surface representation of the electron density map at ~20-Angstrom resoltion for the standard conformation of SR398-GroES-Mg-ATP complex
Sample
  • Sample: ATPase-deficient Single-ring GroEL Mutant SR398 Complexed with GroES under Mg-ATP
  • Protein or peptide: SR398
  • Protein or peptide: GroES
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsChen D-H / Song J-L / Chuang DT / Chiu W / Ludtke SJ
CitationJournal: Structure / Year: 2006
Title: An expanded conformation of single-ring GroEL-GroES complex encapsulates an 86 kDa substrate.
Authors: Dong-Hua Chen / Jiu-Li Song / David T Chuang / Wah Chiu / Steven J Ludtke /
Abstract: Electron cryomicroscopy reveals an unprecedented conformation of the single-ring mutant of GroEL (SR398) bound to GroES in the presence of Mg-ATP. This conformation exhibits a considerable expansion ...Electron cryomicroscopy reveals an unprecedented conformation of the single-ring mutant of GroEL (SR398) bound to GroES in the presence of Mg-ATP. This conformation exhibits a considerable expansion of the folding cavity, with approximately 80% more volume than the X-ray structure of the equivalent cis cavity in the GroEL-GroES-(ADP)(7) complex. This expanded conformation can encapsulate an 86 kDa heterodimeric (alphabeta) assembly intermediate of mitochondrial branched-chain alpha-ketoacid dehydrogenase, the largest substrate ever observed to be cis encapsulated. The SR398-GroES-Mg-ATP complex is found to exist as a mixture of standard and expanded conformations, regardless of the absence or presence of the substrate. However, the presence of even a small substrate causes a pronounced bias toward the expanded conformation. Encapsulation of the large assembly intermediate is supported by a series of electron cryomicroscopy studies as well as the protection of both alpha and beta subunits of the substrate from tryptic digestion.
History
DepositionOct 31, 2006-
Header (metadata) releaseNov 2, 2006-
Map releaseNov 15, 2006-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.10861
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5.10861
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-1aon
  • Surface level: 5.10861
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1286.gif

Downloads & links

-
Map

FileDownload / File: emd_1286.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the surface representation of the electron density map at ~20-Angstrom resoltion for the standard conformation of SR398-GroES-Mg-ATP complex
Voxel sizeX=Y=Z: 2.167 Å
Density
Contour Level1: 2.3 / Movie #1: 5.10861
Minimum - Maximum-3.26905 - 9.470079999999999
Average (Standard dev.)-0.00513377 (±1.29276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 275.209 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.1672.1672.167
M x/y/z127127127
origin x/y/z0.0000.0000.000
length x/y/z275.209275.209275.209
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-3.2699.470-0.005

-
Supplemental data

-
Sample components

-
Entire : ATPase-deficient Single-ring GroEL Mutant SR398 Complexed with Gr...

EntireName: ATPase-deficient Single-ring GroEL Mutant SR398 Complexed with GroES under Mg-ATP
Components
  • Sample: ATPase-deficient Single-ring GroEL Mutant SR398 Complexed with GroES under Mg-ATP
  • Protein or peptide: SR398
  • Protein or peptide: GroES

-
Supramolecule #1000: ATPase-deficient Single-ring GroEL Mutant SR398 Complexed with Gr...

SupramoleculeName: ATPase-deficient Single-ring GroEL Mutant SR398 Complexed with GroES under Mg-ATP
type: sample / ID: 1000
Details: The two components for the sample were mixed with Mg-ATP at Room Temperature
Oligomeric state: One heptamer of GroES binds to one heptamer of SR398
Number unique components: 2
Molecular weightExperimental: 470 KDa / Theoretical: 470 KDa

-
Macromolecule #1: SR398

MacromoleculeName: SR398 / type: protein_or_peptide / ID: 1 / Details: This is the GroEL protein with D398A mutation / Number of copies: 1 / Oligomeric state: Heptamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / synonym: E. coli / Cell: E.coli / Organelle: cytoplasm / Location in cell: cytoplasm
Molecular weightExperimental: 400 KDa / Theoretical: 400 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: PET

-
Macromolecule #2: GroES

MacromoleculeName: GroES / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: heptamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / synonym: E. coli / Cell: E.coli / Organelle: cytoplasm / Location in cell: cytoplasm
Molecular weightExperimental: 70 KDa / Theoretical: 70 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pACYC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 50mM KPi, 150mM NaCl, 0.02% NaN3
GridDetails: 400 mesh quantifoil grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 95 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot
Method: Blot twice and 1.5 seconds for each blot before plunging.

-
Electron microscopy

MicroscopeJEOL 2010F
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at
DateSep 10, 2003
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Average electron dose: 18 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.95 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN

+
Image processing

DetailsThe particles were selected semi-automatically.
CTF correctionDetails: whole CCD frame
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 6081
Final angle assignmentDetails: EMAN
Final two d classificationNumber classes: 257

-
Atomic model buiding 1

Initial modelPDB ID:

1aon

SoftwareName: foldhunter
DetailsProtocol: Rigid Body. The GroEL trans ring of 1AON structure was removed during fitting
RefinementProtocol: RIGID BODY FIT

+
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://pdbjlvh1.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