PDB-3ktt: Atomic model of bovine TRiC CCT2(beta) subunit derived ...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3ktt
Title	Atomic model of bovine TRiC CCT2(beta) subunit derived from a 4.0 Angstrom cryo-EM map
Descriptor	T-complex protein 1 subunit beta
Keywords	CHAPERONE, TRiC/CCT, CCT2(beta), cryo-EM, ATP-binding, Chaperone, Nucleotide-binding
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-5145, Made by Jmol #3: Superimposing with simplified surface model of EM map, EMDB-5148, Made by Jmol #4: Superimposing with EM 3D map: EMDB-5145, Made by UCSF CHIMERA #5: Superimposing with EM 3D map: EMDB-5148, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-5145 Fit EMDB-5148 Fit PDB-3iyg Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-1649 PDB-3j25 PDB-3iym PDB-3dkn List of similar structure data about Omokage system

Article
Citation - primary
Article	Proc.Natl.Acad.Sci.USA, Vol. 107, Page: 4967 - 4972, Year: 2010,
Title	4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.
Authors	Cong, Y., Baker, M.L., Jakana, J., Woolford, D., Miller, E.J., Reissmann, S., Kumar, R.N., Redding-Johanson, A.M., Batth, T.S., Mukhopadhyay, A., Ludtke, S.J., Frydman, J., Chiu, W.
Links	DOI: 10.1073/pnas.0913774107
Citation - 1
Article	To be Published, Vol. , Page: - , Year: ,
Title	To be published
Authors	Cong, Y., Baker, M.L., Jakana, J., Woolford, D., Miller, E.J., Reissmann, S., Kumar, R.N., Redding-Johanson, A.M., Batth, T.S., Mukhopadhyay, A., Ludtke, S.J., Frydman, J., Chiu, W.

Components
ID 1 : TCP-1-beta, CCT-beta
Image
Description	T-complex protein 1 subunit beta
Type	polypeptide(L)
Formula weight	55107.824 Da
Number of molecules	1
ID	1
Source	Method: Isolated from a natural source Common name: bovine NCBI taxonomy: ID:9913 Organism scientific: Bos taurus
Links	UniProt: Q3ZBH0, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	CCT2(beta) subunit in the both-ring closed bovine TRiC complex
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Vitrification
Details	vitrification using ethane as cryogen
Experiment
Method	ELECTRON MICROSCOPY

Processing
2D projection selection
Software name	COOT, Chimera, Modeller
3D reconstruction
Actual pixel size	1.2 A/pix
CTF correction method	FSC at 0.5 cut-off
Details	Single particle 3D reconstruction using EMAN1.8+ with our recently developed 2-D fast rotation matching method (FRM2D) for the image alignment.
Method	Projection matching
Resolution	4.0 A
3D fitting
Method	Local refinement, Flexible fitting
Refinement Protocol	Local refinement, Flexible fitting
Refinement Space	REAL
Software name	COOT, Chimera, Modeller
3D fitting list
3D fitting id	1
Refine hist
Cycle id	LAST
Refine id	ELECTRON MICROSCOPY
Total atoms	3855
Protein atoms	3855

PDB format

All

Header only

mmCIF format

mmCIF

XML format

All

No-atom

Ext-atom

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 2.5 MB .webm (WebM/VP8 format), 3.4 MB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 4.5 MB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 4.6 MB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 4.5 MB

movie #5

	.mp4 (H.264/MPEG-4 AVC format), 3.7 MB .webm (WebM/VP8 format), 5.1 MB