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model refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP

by single particle reconstruction, at 10.7 A resolution

Movie

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#1: Depositted structure unit, Made by Jmol

#2: Superimposing with EM 3D map: EMDB-1961, Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4a0v
Titlemodel refined against the Symmetry-free cryo-EM map of TRiC-AMP-PNP
DescriptorT-COMPLEX PROTEIN 1 SUBUNIT BETA
KeywordsCHAPERONE, CHAPERONIN, PROTEIN FOLDING
AuthorsCong, Y., Schroder, G.F., Meyer, A.S., Jakana, J., Ma, B., Dougherty, M.T., Schmid, M.F., Reissmann, S., Levitt, M., Ludtke, S.L., Frydman, J., Chiu, W.
DateDeposition: 2011-09-13, Release: 2012-02-15
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-1961, Made by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-1961

CiteFit

Cite: data citing same article

Fit: target map of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - primary
ArticleEMBO J., Vol. 31, Issue 3, Page 720-30, Year 2012
TitleSymmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle.
AuthorsYao Cong, Gunnar F Schröder, Anne S Meyer, Joanita Jakana, Boxue Ma, Matthew T Dougherty, Michael F Schmid, Stefanie Reissmann, Michael Levitt, Steven L Ludtke, Judith Frydman, Wah Chiu
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.
KeywordsAdenosine Triphosphatases (metabolism, 3.6.1.-), Chaperonins (chemistry, 3.6.1.-), Cryoelectron Microscopy, Hydrolysis, Models, Molecular, Protein Conformation, Protein Folding
LinksDOI: 10.1038/emboj.2011.366, PubMed: 22045336, PMC: PMC3273382
Components
ID 1 : TCP-1-BETA, CCT-BETA, BOVINE TRIC
Image
DescriptionT-COMPLEX PROTEIN 1 SUBUNIT BETA
Typepolypeptide(L)
Formula weight55107.824 Da
Number of molecules16
ID1
SourceMethod: Isolated from a natural source
Common name: CATTLE
NCBI taxonomy: ID:9913
Organ: TESTES
Organism scientific: BOS TAURUS

LinksUniProt: Q3ZBH0, Sequence view
Sample
Assembly
Aggregation statePARTICLE
NameBOVINE TRIC IN THE AMP- PNP STATE
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE
Sample support
DetailsHOLEY CARBON
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: OTHER
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose18 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationNominal: 50000 X
CsNominal: 4.1 mm
Nominal defocusMax: 3000 nm, Min: 1200 nm
Specimen holder
Temperature101 Kelvin
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images700
Processing
2D projection selection
Number of particles29374
Software nameEMAN1.8
Single particle entity
Symmetry typeMIXED SYMMETRY
3D reconstruction
Actual pixel size2.4 A/pix
CTF correction methodEACH MICROGRAPH
DetailsOUR MODELS DO NOT INCLUDE SOME REGIONS OF THE APICAL DOMAIN IN SEVERAL SUBUNITS BECAUSE THE MAP IN THOSE REGIONS WAS NOT VERY WELL RESOLVED DUE TO THE DYNAMIC NATURE OF THOSE SUBUNITS. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD- 1961. (DEPOSITION ID: 10236).
MethodPROJECTION MATCHING
Nominal pixel size2.4 A/pix
Resolution10.7 A
Refine
Refine idELECTRON MICROSCOPY
Ls d res high10.70 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high10.70
Total atoms59707
Protein atoms59707
Download
PDB format
Allpdb4a0v.ent.gz
pdb4a0v.ent (uncompressed file)
Header onlypdb4a0v.ent.gz
mmCIF format
mmCIF4a0v.cif.gz
XML format
All4a0v.xml.gz
No-atom4a0v-noatom.xml.gz
Ext-atom4a0v-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.2 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB