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C7 Symmetrized Structure of Unliganded GroEL at 4.7 Angstrom Resolution from CryoEM

by single particle reconstruction, at 4.7 A resolution

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#1: Deposited structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-5002, Image by UCSF CHIMERA

#3: Superimposing with EM 3D map: EMDB-5002, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3c9v
TitleC7 Symmetrized Structure of Unliganded GroEL at 4.7 Angstrom Resolution from CryoEM
Descriptor60 kDa chaperonin
KeywordsCHAPERONE, GroEL, ATP-binding, Cell cycle, Cell division, Chaperone, Nucleotide-binding, Phosphoprotein
AuthorsLudtke, S.J., Baker, M.L., Chen, D.H., Song, J.L., Chuang, D., Chiu, W.
DateDeposition: 2008-02-18, Release: 2008-09-02
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-5002, Image by UCSF CHIMERA

#3: Superimposing with EM 3D map: EMDB-5002, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-5002

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Article
Citation - primary
ArticleStructure, Vol. 16, Issue 3, Page 441-8, Year 2008
TitleDe novo backbone trace of GroEL from single particle electron cryomicroscopy.
AuthorsSteven J Ludtke, Matthew L Baker, Dong-Hua Chen, Jiu-Li Song, David T Chuang, Wah Chiu
KeywordsChaperonin 10 (chemistry), Chaperonin 60 (chemistry), Dimerization, Escherichia coli, Imaging, Three-Dimensional, Microscopy, Electron (methods), Models, Molecular, Molecular Chaperones (chemistry), Signal Transduction (physiology)
LinksPII: S0969-2126(08)00072-5, DOI: 10.1016/j.str.2008.02.007, PubMed: 18334219
Components
ID 1 : Protein Cpn60, groEL protein
Image
Description60 kDa chaperonin
Typepolypeptide(L)
Fragmentresidues 2-527
Formula weight55463.934 Da
Number of molecules14
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: groL, groEL, mopA, Escherichia coli
Host: Escherichia coli

, ESts CG-712, plasmid
Plasmid name: pGroESL
LinksUniProt: P0A6F5, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameGroEL
Entity assembly
Assembly-ID1
Details14-mer. Two back to back homo-heptameric rings.
GO-IDGO:0006457
InterPro-IDIPR:012723
NameGroEL
Buffer
Name20 mM Tris.HCl, pH 7.5, 50 mM MgCl2
Sample preparation
pH7.5
Vitrification
DetailsETHANE. Vitrobot, blot for 2 sec.
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: JEOL 3200SFF
Date2005
Electron gun
Electron sourceField Emission Gun
Accelerating voltage300 kV
Electron dose36 e/A**2
Illumination modeFlood Beam
Lens
ModeBright Field
MagnificationNominal: 60000 X
CsNominal: 1.6 mm
Nominal defocusMax: 2300 nm, Min: 900 nm
Specimen holder
Tilt angleMin: 0 degrees, Max: 0 degrees
Temperature4 Kelvin
Detector
TypeKodak SO163 film
Processing
3D reconstruction
CTF correction methodper micrograph
DetailsC7 symmetry, This entry contains CA atom only
MethodEMAN, single particle
Nominal pixel size1.06 A/pix
Resolution4.7 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms7364
Protein atoms7364
Download
PDB format
Allpdb3c9v.ent.gz
pdb3c9v.ent (uncompressed file)
Header onlypdb3c9v.ent.gz
mmCIF format
mmCIF3c9v.cif.gz
XML format
All3c9v.xml.gz
No-atom3c9v-noatom.xml.gz
Ext-atom3c9v-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.2 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 6 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5 MB