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ATP-bound states of GroEL captured by cryo-electron microscopy.

by single particle reconstruction, at 23.5 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.08, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.08, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1gru, Surface level: 0.08, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1046
TitleATP-bound states of GroEL captured by cryo-electron microscopy.
MapGroEL with GroES and ADP bound to one ring, and ATP bound to the other ring
SampleGroES-ADP7-GroEL-ATP7 from E.coli
AuthorsSaibil HR
DateDeposition: 2003-03-13, Header release: 2003-05-16, Map release: 2003-05-16, 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: 0.08, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.08, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-1gru, Surface level: 0.08, Image by UCSF CHIMERA

Supplemental images
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Related Structure Data
Related Entries

PDB-1gru

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Article
Citation - Primary
ArticleCell, Vol. 107, Issue 7, Page 869-79, Year 2001
TitleATP-bound states of GroEL captured by cryo-electron microscopy.
AuthorsN A Ranson, G W Farr, A M Roseman, B Gowen, W A Fenton, A L Horwich, H R Saibil
Department of Crystallography, Birkbeck College London, Malet Street, London WC1E 7HX, United Kingdom.
KeywordsAdenosine Triphosphate (chemistry), Chaperonin 60 (chemistry), Cryoelectron Microscopy, Escherichia coli, Models, Molecular, Protein Binding, Protein Folding
LinksPubMed: 11779463, PII: S0092-8674(01)00617-1
Map
Fileemd_1046.map.gz ( map file in CCP4 format, 8193 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.8 A/pix
= 358.4 A
128 pix
2.8 A/pix
= 358.4 A
128 pix
2.8 A/pix
= 358.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.029 (by author), 0.08 (movie #1):
Minimum - Maximum: -0.04720771 - 0.27609465
Average (Standard dev.): 0.00606513 (0.02973022)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
Unit CellA= B= C: 358.4 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.8 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.82.82.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ0052
NX/NY/NZ12812855
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0470.2760.006
Annotation DetailsGroEL with GroES and ADP bound to one ring, and ATP bound to the other ring
Supplement
Images
Images
Sample
NameGroES-ADP7-GroEL-ATP7 from E.coli
Oligomeric State14-mer
Number of Components2
Experimental Mass1MDa
Theoretical Mass1MDa
DetailsThe complexes were prepared by pre-forming a GroEL-GroES-ADP complex, with 100 uM ADP, then adding an excess of single ring GroEL (SR1) to trap any released GroES; then 1 mM ATP was added. Any GroEL-GroES complexes remaining have ADP in the GroES-bound ring and ATP in the other ring, modelling the in vivo ATP-binding reaction.
Component #1: protein - Chaperonin 60
Scientific nameGroEL
Common NameChaperonin 60
Theoretical Mass0.8 MDa
Experimental Mass0.8 MDa
Oligomeric Details14-mer
Number of Copies1
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
Recombinant expressionYes
Natural SourceCell: E. coli
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #2: protein - Chaperonin 10
Scientific nameGroES
Common NameChaperonin 10
Theoretical Mass0.07 MDa
Experimental Mass0.07 MDa
Oligomeric Details7-mer
Number of Copies1
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Conc0.8 mg/ml
Specimen Support Detailsholey carbon film
Specimen Stateparticle
BufferDetails: 12.5 mM HEPES, 5 mM KCl, 5 mM MgCl2, 100 uM ADP, then 2x molar excess of single ring mutant of GroEL (SR1), then 1 mM ATP just before vitrification. See sample details for an explanation of the experimental design.
pH: 7.5
Vitrification
Cryogen NameETHANE
Temperature100 Kelvin
InstrumentHOMEMADE PLUNGER
MethodBlot for 1 second before plunging
Time Resolved StateThe sample was vitrified within a few seconds of manually mixing in ATP.
DetailsVitrification instrument: self made
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus900 nm - 3000 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Temperature105 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images71
Sampling Size14
Od Range1
Quant Bit Number8
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection matching
SoftwareSpider
CTF CorrectionCTF multiplication and merging of 2D averages
Resolution By Author23.5 A
Resolution MethodFSC 0.5
Euler Angles DetailsFull coverage around a single axis, using mainly side views
DetailsFiltered back projection
Single Particle
Number of Projections1448
Applied SymmetryC7 (7 fold cyclic)
Atomic Model Fitting
Model #0
Refinement Protocolrigid body
SoftwareManual fitting in O
Refinement SpaceREAL
DetailsProtocol: Rigid body. The only movement relative to the crystal structure of GroEL-ES-ADP seen at this resolution is a twist of the free apical domains.
PDB Entry ID1AON
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1046.xml (9.4 KB)
Map dataemd_1046.map.gz (7.6 MB)
Images1046.gif (26.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1046
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.1 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 6.4 MB