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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, Image by UCSF CHIMERA

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

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

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

#3: Surface view with fitted model, atomic models: PDB-4a0v, Surface level: 1.13, Image 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

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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
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
#1
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