[English] 日本語
Yorodumi
- EMDB-1546: Structure of GroEL in complex with Bacteriophage T4 co-chaperone ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1546
TitleStructure of GroEL in complex with Bacteriophage T4 co-chaperone gp31 and ADPAlF3
Map dataVolume contains GroEL complexed with gp31 without applied symmetry
Sample
  • Sample: GroEL-gp31-ADPALF3
  • Protein or peptide: GroEL
  • Protein or peptide: gp31
  • Ligand: ADPAlF3
Keywordschaperonin / bacteriophage T4 / capsid protein gp23 / GroEL
Function / homologyBacteriophage T4, Gp31, chaperonin-GroEL / protein binding / Chaperonin Cpn60/GroEL
Function and homology information
Biological speciesEscherichia coli (E. coli) / Enterobacteria phage T4 (virus) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 10.5 Å
AuthorsClare DK / Bakkes PJ / van Heerikhuizen H / van der Vies SM / Saibil HR
CitationJournal: Nature / Year: 2009
Title: Chaperonin complex with a newly folded protein encapsulated in the folding chamber.
Authors: D K Clare / P J Bakkes / H van Heerikhuizen / S M van der Vies / H R Saibil /
Abstract: A subset of essential cellular proteins requires the assistance of chaperonins (in Escherichia coli, GroEL and GroES), double-ring complexes in which the two rings act alternately to bind, ...A subset of essential cellular proteins requires the assistance of chaperonins (in Escherichia coli, GroEL and GroES), double-ring complexes in which the two rings act alternately to bind, encapsulate and fold a wide range of nascent or stress-denatured proteins. This process starts by the trapping of a substrate protein on hydrophobic surfaces in the central cavity of a GroEL ring. Then, binding of ATP and co-chaperonin GroES to that ring ejects the non-native protein from its binding sites, through forced unfolding or other major conformational changes, and encloses it in a hydrophilic chamber for folding. ATP hydrolysis and subsequent ATP binding to the opposite ring trigger dissociation of the chamber and release of the substrate protein. The bacteriophage T4 requires its own version of GroES, gp31, which forms a taller folding chamber, to fold the major viral capsid protein gp23 (refs 16-20). Polypeptides are known to fold inside the chaperonin complex, but the conformation of an encapsulated protein has not previously been visualized. Here we present structures of gp23-chaperonin complexes, showing both the initial captured state and the final, close-to-native state with gp23 encapsulated in the folding chamber. Although the chamber is expanded, it is still barely large enough to contain the elongated gp23 monomer, explaining why the GroEL-GroES complex is not able to fold gp23 and showing how the chaperonin structure distorts to enclose a large, physiological substrate protein.
History
DepositionSep 2, 2008-
Header (metadata) releaseSep 3, 2008-
Map releaseApr 2, 2009-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1546.gif

Downloads & links

-
Map

FileDownload / File: emd_1546.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume contains GroEL complexed with gp31 without applied symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
2.8 Å/pix.
x 160 pix.
= 448. Å		2.8 Å/pix.
x 160 pix.
= 448. Å		2.8 Å/pix.
x 160 pix.
= 448. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0823 / Movie #1: 0.15
Minimum - Maximum-2.12056 - 3.95521
Average (Standard dev.)0.00561715 (±0.0925135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-81-81-81
Dimensions160160160
Spacing160160160
CellA=B=C: 448 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z448.000448.000448.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S213
start NC/NR/NS-81-81-81
NC/NR/NS160160160
D min/max/mean-2.1213.9550.006

-
Supplemental data

-
Sample components

-
Entire : GroEL-gp31-ADPALF3

EntireName: GroEL-gp31-ADPALF3
Components
  • Sample: GroEL-gp31-ADPALF3
  • Protein or peptide: GroEL
  • Protein or peptide: gp31
  • Ligand: ADPAlF3

-
Supramolecule #1000: GroEL-gp31-ADPALF3

SupramoleculeName: GroEL-gp31-ADPALF3 / type: sample / ID: 1000 / Details: Empty Chaperonin
Oligomeric state: tetradecamer of GroEL bound to a heptamer of gp31
Number unique components: 3
Molecular weightExperimental: 900 KDa / Theoretical: 900 KDa / Method: sequence

-
Macromolecule #1: GroEL

MacromoleculeName: GroEL / type: protein_or_peptide / ID: 1 / Name.synonym: GroEL / Number of copies: 1 / Oligomeric state: tetradecamer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MC1009 / Location in cell: cytoplasm
Molecular weightExperimental: 56 KDa / Theoretical: 56 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pSL6
SequenceGO: protein binding / InterPro: Chaperonin Cpn60/GroEL

-
Macromolecule #2: gp31

MacromoleculeName: gp31 / type: protein_or_peptide / ID: 2 / Name.synonym: Bacteriophage T4 co-chaperonin / Number of copies: 1 / Oligomeric state: heptamer / Recombinant expression: Yes
Source (natural)Organism: Enterobacteria phage T4 (virus) / synonym: Bacteriophage T4 / Location in cell: cytoplasmic
Molecular weightExperimental: 12 KDa / Theoretical: 12 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pAR1
SequenceInterPro: Bacteriophage T4, Gp31, chaperonin-GroEL

-
Macromolecule #3: ADPAlF3

MacromoleculeName: ADPAlF3 / type: ligand / ID: 3 / Name.synonym: Non-hydrolysable ATP analogue / Number of copies: 14 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: synthetic construct (others)

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Details: 40 mM Tris-HCl pH 7.5, 10 mM KCl, 10 mM MgCl2, 2.5 mM ADPAlF3 After nucleotide addition the sample was incubated for 15 minutes before vitrification
StainingType: NEGATIVE / Details: Cryo
GridDetails: 400 mesh R2/2 c-flat grids
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger / Method: blot for 2-3 seconds before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: corrected at 150,00 times
DateJun 1, 2006
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 1.4 µm / Number real images: 150 / Average electron dose: 15 e/Å2 / Od range: 0.5 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

DetailsNo symmetry was applied
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Details: No symmetry was applied to the reconstruction / Number images used: 7400
Final angle assignmentDetails: SPIDER:theta 90-110 degrees, phi 0-360 degrees. Mirror option was on.

-
Atomic model buiding 1

Initial modelPDB ID:

2cgt

SoftwareName: URO
DetailsProtocol: Individual domains fitted as rigid bodies. The domains were separately fitted in URO
RefinementSpace: RECIPROCAL / 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