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Symmetry-free cryo-EM map of TRiC-AMP-PNP

by single particle reconstruction, at 10.7 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.13, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.13, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4a0v, Surface level: 1.13, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1961
TitleSymmetry-free cryo-EM map of TRiC-AMP-PNP
Mapsymmetry-free cryo-EM density of TRiC-AMP-PNP
Samplebovine TRiC/CCT in the AMP-PNP state
KeywordsTRiC/CCT, chaperonin, cryo-EM, protein folding
AuthorsCong Y, Schroder GF, Meyer AS, Jakana J, Ma B, Dougherty MT, Schmid MF, Reissmann S, Levitt M, Ludtke SL, Frydman J, Chiu W
DateDeposition: 2011-09-05, Header release: 2012-02-06, Map release: 2012-02-06, Last update: 2013-03-20
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.13, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 1.13, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4a0v, Surface level: 1.13, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-4a0v

CiteFit

Cite: data citing same article

Fit: output model 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
Map
Fileemd_1961.map.gz ( map file in CCP4 format, 11665 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
2.4 A/pix
= 345.6 A
144 pix
2.4 A/pix
= 345.6 A
144 pix
2.4 A/pix
= 345.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1.13 (by author), 1.13 (movie #1):
Minimum - Maximum: -0.37267885 - 2.16418886
Average (Standard dev.): 0.06878981 (0.26539356)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions144144144
Origin-72-72-72
Limit717171
Spacing144144144
Unit CellA= B= C: 345.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.4 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.42.42.4
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.3732.1640.069
Annotation Detailssymmetry-free cryo-EM density of TRiC-AMP-PNP
Supplement
Images
Images
Sample
Namebovine TRiC/CCT in the AMP-PNP state
Number of Components2
Oligomeric State16-mer
Theoretical Mass1MDa
Experimental Mass1MDa
Component #1: protein - TRiC or CCT
Scientific namebovine TRiC
Common NameTRiC or CCT
Theoretical Mass1 MDa
Experimental Mass1 MDa
Oligomeric Details16-mer
Scientific Name of SpeciesBos taurus

Common Name of Speciesbovine
NCBI taxonomy9913
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Conc1 mg/ml
Specimen Support Details200-mesh Quantifoil holey grid
Specimen Stateparticle
Vitrification
MethodTwo-side blotting for 1 second before plunging
Cryogen NameETHANE
DetailsVitrification instrument: FEI vitrobot
Humidity100
InstrumentFEI VITROBOT
Temperature101 Kelvin
Imaging
MicroscopeJEOL 3200FSC
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose18 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
AstigmatismObjective lens astigmatism correction
Nominal Cs4.1 mm
Imaging ModeBRIGHT FIELD
Defocus1200 nm - 3000 nm
Energy FilterEnergy Filter: JEOL in-column omega energy filter , Energy Window: 0-20 eV
Specimen Holder
HolderSide entry
ModelJEOL 3200FSC CRYOHOLDER
Tilt Angle0 degrees - 0 degrees
Temperature101 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerNIKON SUPER COOLSCAN 9000
Number of Digital Images700
Sampling Size6.35
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmprojection matching
SoftwareEMAN1.8
CTF Correctioneach 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
Resolution By Author10.7 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections29374
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1961.xml (7.5 KB)
Map dataemd_1961.map.gz (10.3 MB)
Imagesimage1961.png (105.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1961
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.8 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 6.2 MB