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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: Depositted structure unit, Made by Jmol

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

#3: Superimposing with EM 3D map: EMDB-5002, Made 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, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Made by Jmol

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

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

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Related Structure Data
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EMDB-5002

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List of similar structure data about Omokage system
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
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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), 4.1 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