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Structure of GroEL in complex with non-native capsid protein gp23, Bacteriophage T4 co-chaperone gp31 and ADPAlF3

by single particle reconstruction, at 10.2 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.15, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.15, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-2cgt, Surface level: 0.15, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1547
TitleStructure of GroEL in complex with non-native capsid protein gp23, Bacteriophage T4 co-chaperone gp31 and ADPAlF3
MapVolume contains GroEL in complex with non-native capsid protein gp23, co-chaperonin gp31 and ADPAlF3
SampleGroEL-gp31-gp23(1)-ADPALF3
Keywordschaperonin, bacteriophage T4, capsid protein gp23, GroEL, co-chaperone gp31
AuthorsClare DK, Bakkes PJ, van Heerikhuizen H, van der Vies SM, Saibil HR
DateDeposition: 2008-09-02, Header release: 2008-09-03, Map release: 2009-04-02, 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: 0.15, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.15, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-2cgt, Surface level: 0.15, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Fit: output model of fitting

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Article
Citation - Primary
ArticleNature, Vol. 457, Issue 7225, Page 107-10, Year 2009
TitleChaperonin complex with a newly folded protein encapsulated in the folding chamber.
AuthorsD K Clare, P J Bakkes, H van Heerikhuizen, S M van der Vies, H R Saibil
Department of Crystallography and Institute for Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK.
KeywordsCapsid Proteins (chemistry), Chaperonin 10 (chemistry), Chaperonin 60 (chemistry), Models, Molecular, Multiprotein Complexes (chemistry), Protein Folding, Viral Proteins (chemistry), gene 31 protein, Enterobacteria phage T4, gp23 protein, Bacteriophage T4
LinksDOI: 10.1038/nature07479, PubMed: 19122642, PMC: PMC2728927
Map
Fileemd_1547.map.gz ( map file in CCP4 format, 16001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)X (Row.)Y (Col.)
160 pix
2.8 A/pix
= 448. A
160 pix
2.8 A/pix
= 448. A
160 pix
2.8 A/pix
= 448. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.0947, 0.15 (movie #1):
Minimum - Maximum: -1.94969 - 3.39623
Average (Standard dev.): 0.00648203 (0.0950591)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions160160160
Origin-81-81-81
Limit787878
Spacing160160160
Unit CellA= B= C: 448 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/z160160160
origin x/y/z0.0000.0000.000
length x/y/z448.000448.000448.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-81-81-81
NX/NY/NZ160160160
MAP C/R/S213
start NC/NR/NS-81-81-81
NC/NR/NS160160160
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-1.9503.3960.006
Annotation DetailsVolume contains GroEL in complex with non-native capsid protein gp23, co-chaperonin gp31 and ADPAlF3
Supplement
Images
Images
Sample
NameGroEL-gp31-gp23(1)-ADPALF3
Number of Components4
Oligomeric Statetetradecamer of GroEL bound to a heptamer of gp31 and a monomer of gp23
Theoretical Mass0.95MDa
Detailsone copy of gp23 is bound to GroEL in the opposite ring to that of the co-chaperonin gp31
Mass-estimation Methodsequence
Experimental Mass0.95MDa
Component #1: protein - GroEL
Scientific nameGroEL
Theoretical Mass0.056 MDa
Experimental Mass0.056 MDa
Oligomeric Detailstetradecamer
Number of Copies1
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
StrainMC1009
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceVector: pSL6
NCBI taxonomy: 562
Expression system: Escherichia coli
LinksGene Ontology: GO:0005515, Inter Pro: IPR:001844
Component #2: protein - bacteriophage T4 co-chaperonin
Scientific namegp31
Common Namebacteriophage T4 co-chaperonin
Theoretical Mass0.012 MDa
Experimental Mass0.012 MDa
Oligomeric Detailsheptamer
Number of Copies1
Scientific Name of SpeciesEnterobacteria phage T4
Common Name of SpeciesBacteriophage T4
NCBI taxonomy10665
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Vector: pAR1
LinksInter Pro: IPR:016416
Component #3: protein - Major capsid protein
Scientific namegp23
Common NameMajor capsid protein
Theoretical Mass0.056 MDa
Experimental Mass0.056 MDa
Oligomeric Detailsmonomer
Number of Copies1
Scientific Name of SpeciesEnterobacteria phage T4
Common Name of SpeciesBacteriophage T4
NCBI taxonomy10665
Recombinant expressionYes
Natural SourceCell Location: Cytoplasm
Engineered SourceVector: pET2331
NCBI taxonomy: 562
Expression system: Escherichia coli
LinksInter Pro: IPR:010762
Component #4: ligand - Non-hydrolysable ATP analogue
Scientific nameADPAlF3
Common NameNon-hydrolysable ATP analogue
Oligomeric Detailsmonomer
Number of Copies14
Scientific Name of Speciessynthetic construct
NCBI taxonomy32630
Recombinant expressionNo
Experiment
Sample Preparation
StainingCryo
Specimen Conc1 mg/ml
Specimen Support Details400 mesh R2/2 c-flat grids
Specimen Stateparticle
BufferDetails: 40 mM Tris-HCl pH 7.5, 10 mM KCl, 10 mM MgCl2, 2.5 mM ADPAlF3 After nucleotide addition the sample was incubated for 15 minutes before vitrification
pH: 7.5
Vitrification
Methodblot for 2-3 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: manual plunger
InstrumentHOMEMADE PLUNGER
Temperature100 Kelvin
Imaging
MicroscopeFEI TECNAI F20
Date01-JUN-2006
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose15 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 50000
Astigmatismcorrected at 150,00 times
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 3000 nm
Specimen Holder
Holderside entry
ModelGATAN LIQUID NITROGEN
Temperature100 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
Od Range0.5
ScannerZEISS SCAI
Number of Digital Images150
Sampling Size1.4
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmSIRT
Euler Angles DetailsSPIDER:theta 90-110 degrees, phi 0-360 degrees. Mirror option was on.
SoftwareSPIDER
CTF CorrectionEach particle
DetailsNo symmetry was applied to the reconstruction
Resolution By Author10.2 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections7300
DetailsNo symmetry was applied
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
Target Criteriacross-correlation coefficient
DetailsProtocol: Individual domains fitted as rigid bodies. The domains were separately fitted in URO
SoftwareURO
Refinement Protocolrigid body
Refinement SpaceRECIPROCAL
PDB Entry ID2CGT
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1547.xml (11.6 KB)
Map dataemd_1547.map.gz (229 KB)
Images1547.gif (42.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1547
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, 19.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 19.8 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 6.1 MB