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ATP-triggered molecular mechanics of the chaperonin GroEL

by single particle reconstruction, at 8.5 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.2, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.2, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4aau, Surface level: 0.2, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2001
TitleATP-triggered molecular mechanics of the chaperonin GroEL
MapThe GroEL-ATP14 Rd1-Rd3 map is one of seven maps calculated from a heterogenous sample
SampleGroEL-ATP14 Rd1-Rd3
KeywordsTetradecamer of GroEL with ATP bound in both ring
AuthorsClare DK, Vasishtan D, Stagg S, Quispe J, Farr GW, Topf M, Horwich AL, Saibil HR
DateDeposition: 2011-12-02, Header release: 2011-12-16, Map release: 2012-04-17, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.2, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.2, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4aau, Surface level: 0.2, Made by UCSF CHIMERA

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

PDB-4aau

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
ArticleCell, Vol. 149, Issue 1, Page 113-23, Year 2012
TitleATP-triggered conformational changes delineate substrate-binding and -folding mechanics of the GroEL chaperonin.
AuthorsDaniel K Clare, Daven Vasishtan, Scott Stagg, Joel Quispe, George W Farr, Maya Topf, Arthur L Horwich, Helen R Saibil
Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK.
KeywordsAdenosine Triphosphate (metabolism), Bacteria (chemistry), Chaperonin 10 (metabolism), Chaperonin 60 (chemistry), Cryoelectron Microscopy, Escherichia coli (chemistry), Escherichia coli Proteins (chemistry), GroE protein, E coli, Heat-Shock Proteins (chemistry), Hydrophobic and Hydrophilic Interactions, Protein Conformation, Protein Folding
LinksPII: S0092-8674(12)00287-5, DOI: 10.1016/j.cell.2012.02.047, PubMed: 22445172, PMC: PMC3326522
Map
Fileemd_2001.map.gz ( map file in CCP4 format, 27649 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
2.02 A/pix
= 387.84 A
192 pix
2.02 A/pix
= 387.84 A
192 pix
2.02 A/pix
= 387.84 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.2 (by author), 0.2 (movie #1):
Minimum - Maximum: -1.95698512 - 2.98391771
Average (Standard dev.): 0.00926961 (0.1169842)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin-96-96-96
Limit959595
Spacing192192192
Unit CellA= B= C: 387.84 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.02 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.022.022.02
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z387.840387.840387.840
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.9572.9840.009
Annotation DetailsThe GroEL-ATP14 Rd1-Rd3 map is one of seven maps calculated from a heterogenous sample
Supplement
Images
Images
Sample
NameGroEL-ATP14 Rd1-Rd3
Number of Components2
Oligomeric StateTetradecamer of GroEL with 14 ATP molecules bound
Theoretical Mass0.8MDa
Experimental Mass0.8MDa
Component #1: protein - GroEL
Scientific namehsp60
Common NameGroEL
Theoretical Mass0.056 MDa
Experimental Mass0.056 MDa
DetailsATPase Mutant, D398A
Oligomeric Detailstetradecamer
Number of Copies14
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
Recombinant expressionYes
Natural SourceCell Location: cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
LinksGene Ontology: GO:0042026, Inter Pro: IPR:002423
Component #2: ligand - ATP
Scientific nameATP
Theoretical Mass0.00055 MDa
Experimental Mass0.00055 MDa
DetailsATP is bound to all 14 subunits
Scientific Name of Speciessynthetic construct
NCBI taxonomy32630
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Conc4 mg/ml
Specimen Support Detailscflat grids r2/2
Specimen Stateparticle
BufferDetails: 50 mM Tris-HCl pH 7.4, 50 mM KCl, 10 mM MgCl2 and 200uM ATP
pH: 7.4
Vitrification
Methodgrids were blotted for 2-3 seconds
Cryogen NameETHANE
Time Resolved Statevitrified within 30 seconds
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Temperature95 Kelvin
Imaging
MicroscopeFEI TECNAI F20
DetailsThe data was collected with leginon at SCRIPPS
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationCalibrated: 148500
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus700 nm - 3500 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Temperature95 K ( 95 - 95 K)
Camera
DetectorGATAN ULTRASCAN 4000 (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmprojection matching
Euler Angles Detailstheta 80-100, phi 0-51.42
SoftwareSPIDER, IMAGIC
CTF Correctioneach particle was phase flipped
DetailsSIRT was used to reconstruct the final map
Resolution By Author8.5 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections6500
DetailsThe particles were automatically picked using FindEM
Applied SymmetryC7 (7 fold cyclic)
Atomic Model Fitting
Model #0
Target Criteriacross-correlation coefficient
DetailsProtocol: Flexible fitting
SoftwareChimera, Flex-EM, NAMD2.6
Refinement Protocolflexible
Refinement SpaceREAL
PDB Entry ID1OEL
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-2001.xml (9 KB)
Map dataemd_2001.map.gz (502.9 KB)
ImagesEMD2001.jpeg (29 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2001
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, 26.5 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.6 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.7 MB
Session file for UCSF-Chimera, 5.5 MB