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Ca model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map

by single particle reconstruction, at 4 A resolution

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#1: Deposited structure unit, Image by Jmol

#2: Superimposing with EM 3D map: EMDB-5145, Image by UCSF CHIMERA

#3: Superimposing with EM 3D map: EMDB-5148, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3iyg
TitleCa model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map
DescriptorT-complex protein 1 subunit theta
T-complex protein 1 subunit gamma
T-complex protein 1 subunit zeta
T-complex protein 1 subunit delta
T-complex protein 1 subunit beta
T-complex protein 1 subunit alpha
T-complex protein 1 subunit eta
KeywordsCHAPERONE, TRiC/CCT, Asymmetric, Cryo-EM, subunit arrangement, ATP-binding, Chaperone, Isopeptide bond, Nucleotide-binding, Phosphoprotein, Disulfide bond
AuthorsCong, Y., Baker, M.L., Ludtke, S.J., Frydman, J., Chiu, W.
DateDeposition: 2009-11-28, Release: 2010-03-16
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-5145, Image by UCSF CHIMERA

#3: Superimposing with EM 3D map: EMDB-5148, Image by UCSF CHIMERA

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

EMDB-5145

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EMDB-5148

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Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 107, Issue 11, Page 4967-72, Year 2010
Title4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.
AuthorsYao Cong, Matthew L Baker, Joanita Jakana, David Woolford, Erik J Miller, Stefanie Reissmann, Ramya N Kumar, Alyssa M Redding-Johanson, Tanveer S Batth, Aindrila Mukhopadhyay, Steven J Ludtke, Judith Frydman, Wah Chiu
National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemsitry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030.
KeywordsAmino Acid Sequence, Animals, Cattle, Chaperonin Containing TCP-1 (chemistry, 3.6.1.-), Cryoelectron Microscopy, Crystallography, X-Ray, Models, Molecular, Molecular Sequence Data, Protein Structure, Secondary, Protein Subunits (chemistry), Reproducibility of Results, Static Electricity, Surface Properties
LinksDOI: 10.1073/pnas.0913774107, PubMed: 20194787, PMC: PMC2841888
Components
ID 1 : TCP-1-theta, CCT-theta
Image
DescriptionT-complex protein 1 subunit theta
Typepolypeptide(L)
Formula weight55834.520 Da
Number of molecules1
ID1
SourceMethod: Isolated from a natural source
Common name: bovine
NCBI taxonomy: ID:9913
Organism scientific: Bos taurus

LinksUniProt: Q3ZCI9, Sequence view
ID 2 : TCP-1-gamma, CCT-gamma
Image
DescriptionT-complex protein 1 subunit gamma
Typepolypeptide(L)
Formula weight57486.820 Da
Number of molecules1
ID2
SourceMethod: Isolated from a natural source
Common name: bovine
NCBI taxonomy: ID:9913
Organism scientific: Bos taurus
LinksUniProt: Q3T0K2, Sequence view
ID 3 : TCP-1-zeta, CCT-zeta, CCT-zeta-1
Image
DescriptionT-complex protein 1 subunit zeta
Typepolypeptide(L)
Formula weight56602.930 Da
Number of molecules1
ID3
SourceMethod: Isolated from a natural source
Common name: bovine
NCBI taxonomy: ID:9913
Organism scientific: Bos taurus
LinksUniProt: Q3MHL7, Sequence view
ID 4 : TCP-1-delta, CCT-delta
Image
DescriptionT-complex protein 1 subunit delta
Typepolypeptide(L)
Formula weight56058.527 Da
Number of molecules1
ID4
SourceMethod: Isolated from a natural source
Common name: bovine
NCBI taxonomy: ID:9913
Organism scientific: Bos taurus
LinksUniProt: Q2T9X2, Sequence view
ID 5 : TCP-1-beta, CCT-beta
Image
DescriptionT-complex protein 1 subunit beta
Typepolypeptide(L)
Formula weight55107.824 Da
Number of molecules1
ID5
SourceMethod: Isolated from a natural source
Common name: bovine
NCBI taxonomy: ID:9913
Organism scientific: Bos taurus
LinksUniProt: Q3ZBH0, Sequence view
ID 6 : T-complex protein 1 subunit
Image
DescriptionT-complex protein 1 subunit
Typepolypeptide(L)
Formula weight56752.227 Da
Number of molecules1
ID6
SourceMethod: Isolated from a natural source
Common name: bovine
NCBI taxonomy: ID:9913
Organism scientific: Bos taurus
LinksSequence view
ID 7 : TCP-1-alpha, CCT-alpha
Image
DescriptionT-complex protein 1 subunit alpha
Typepolypeptide(L)
Formula weight57495.941 Da
Number of molecules1
ID7
SourceMethod: Isolated from a natural source
Common name: bovine
NCBI taxonomy: ID:9913
Organism scientific: Bos taurus
LinksUniProt: Q32L40, Sequence view
ID 8 : TCP-1-eta, CCT-eta
Image
DescriptionT-complex protein 1 subunit eta
Typepolypeptide(L)
Formula weight56614.812 Da
Number of molecules1
ID8
SourceMethod: Isolated from a natural source
Common name: bovine
NCBI taxonomy: ID:9913
Organism scientific: Bos taurus
LinksUniProt: Q2NKZ1, Sequence view
Sample
Assembly
Aggregation statePARTICLE
Experimental Mass1.0
Theoretical Mass1.0
Namebovine TRiC (also called CCT)
Num components8
Entity assembly
Assembly-ID1
NameTRiC (also called CCT)
TypePROTEIN
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Vitrification
Cryogen nameETHANE
Detailsvitrification using ethane as cryogen
Humidity95
Methodtwo-side blotting for 1 second before plunging
Temp101 Kelvin
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: JEM3200FSC
DateAug-2007 to Aug-2008
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
Astigmatismobjective lens astigmatism correction
Detector distance0.0
Nominal defocusMax: 3000 nm, Min: 1000 nm
Energy filterin-column omega energy filter
Energy window0-20 eV
Specimen holder
Specimen holderModel: JEM3200FSC CRYOHOLDER, Type: side entry
Tilt angleMin: 0.0 degrees, Max: 0.0 degrees
Temperature101 Kelvin
Detector
TypeKodak SO163 film
Processing
2D projection selection
Software nameCOOT, Chimera, Modeller
3D reconstruction
Actual pixel size1.2 A/pix
CTF correction methodeach micrograph
DetailsA recently developed 2-D fast rotational matching (FRM2D) algorithm for image alignment, available in EMAN 1.8, was adopted in the refinement steps ( Details about the particle: A recently developed 2-D fast rotational matching (FRM2D) algorithm for image alignment, available in EMAN 1.8, was adopted in the refinement steps )
MethodProjection matching
Nominal pixel size1.2 A/pix
Number of particles101000
Resolution4.0 A
Resolution methodFSC at 0.5 cut-off
SoftwareEMAN
3D fitting
MethodLocal refinement, Flexible fitting
Refinement ProtocolLocal refinement, Flexible fitting
Refinement SpaceREAL
Software nameCOOT, Chimera, Modeller
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms4134
Protein atoms4134
Download
PDB format
Allpdb3iyg.ent.gz
pdb3iyg.ent (uncompressed file)
Header onlypdb3iyg.ent.gz
mmCIF format
mmCIF3iyg.cif.gz
XML format
All3iyg.xml.gz
No-atom3iyg-noatom.xml.gz
Ext-atom3iyg-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.6 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.7 MB