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Negative stain EM Map of the AAA protein CbbX, a red-type Rubisco activase from R. sphaeroides

by single particle reconstruction, at 21 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.017, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.017, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3zuh, Surface level: 0.017, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1932
TitleNegative stain EM Map of the AAA protein CbbX, a red-type Rubisco activase from R. sphaeroides
MapNegative stain EM reconstruction of the R. sphaeroides CbbX hexamer
SampleR. sphaeroides CbbX 3D density map.
KeywordsAAA+ protein, ATPase, Rubisco activase
AuthorsMueller-Cajar O, Stotz M, Wendler P, Hartl FU, Bracher A, Hayer-Hartl M
DateDeposition: 2011-07-18, Header release: 2011-08-26, Map release: 2011-11-03, Last update: 2012-09-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.017, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.017, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3zuh, Surface level: 0.017, Image by UCSF CHIMERA

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

PDB-3zuh

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Fit: output model of fitting

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Article
Citation - Primary
ArticleNature, Vol. 479, Issue 7372, Page 194-9, Year 2011
TitleStructure and function of the AAA+ protein CbbX, a red-type Rubisco activase.
AuthorsOliver Mueller-Cajar, Mathias Stotz, Petra Wendler, F Ulrich Hartl, Andreas Bracher, Manajit Hayer-Hartl
KeywordsAdenosine Triphosphate (metabolism), Allosteric Regulation (drug effects), Bacterial Proteins (chemistry), Carbon Dioxide (metabolism), CbbX protein, Rhodobacter sphaeroides, Crystallography, X-Ray, Enzyme Activation (drug effects), Models, Molecular, Protein Multimerization (drug effects), Protein Structure, Quaternary (drug effects), Rhodobacter sphaeroides (enzymology), Ribulose-Bisphosphate Carboxylase (metabolism, 4.1.1.39), Ribulosephosphates (metabolism), Structure-Activity Relationship, ribulose-1,5 diphosphate (2002-28-0)
LinksDOI: 10.1038/nature10568, PubMed: 22048315
Map
Fileemd_1932.map.gz ( map file in CCP4 format, 8193 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
3.31 A/pix
= 423.68 A
128 pix
3.31 A/pix
= 423.68 A
128 pix
3.31 A/pix
= 423.68 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.005 (by emdb), 0.017 (movie #1):
Minimum - Maximum: -0.011328 - 0.197363
Average (Standard dev.): 0.000343572 (0.00533179)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
Unit CellA= B= C: 423.68 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.31 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z3.313.313.31
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z423.680423.680423.680
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
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-0.0110.1970.000
Annotation DetailsNegative stain EM reconstruction of the R. sphaeroides CbbX hexamer
Supplement
Images
Images
Sample
NameR. sphaeroides CbbX 3D density map.
Number of Components1
Oligomeric StateHexamer
Theoretical Mass0.206MDa
Component #1: protein - CbbX
Scientific nameRubisco Activase
Common NameCbbX
Theoretical Mass0.206 MDa
DetailsThe protein is bound to Ribulose-1,5-bisphosphate, ATP and ATPgammaS
Oligomeric DetailsHexamer
Number of Copies6
Scientific Name of SpeciesRhodobacter sphaeroides
NCBI taxonomy1063
Recombinant expressionYes
Engineered SourceVector: pHue
NCBI taxonomy: 469008
Expression system: Escherichia coli BL21(DE3)
LinksGene Ontology: GO:0005524
Experiment
Sample Preparation
StainingGrids with adsorbed protein stained with 2% (w/v) uranyl acetate for 40 seconds.
Specimen Conc0.072 mg/ml
Specimen Support Detailsplain carbon grid
Specimen Stateparticle
BufferDetails: 20 mM Tris pH 8.0, 50 mM NaCl, 5mM MgCl2, 1mM Ribulose-1,5-bisphosphate, 1mM ATP/ATPgammaS
pH: 8
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 12
Date19-Nov-2010
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 90600, Calibrated: 90600
Astigmatismobjective lens astigmatism was corrected for at 110k magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus260 nm - 1800 nm
Specimen Holder
HolderEucentric
ModelSIDE ENTRY, EUCENTRIC
Camera
DetectorFEI EAGLE (2k x 2k)
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmangular reconstitution
SoftwareMRC, IMAGIC, SPIDER
CTF Correctionphase flipping, each particle
Resolution By Author21 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections245
Applied SymmetryC6 (6 fold cyclic)
Atomic Model Fitting
Model #0
DetailsProtocol: rigid body
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID3SYL
Model #1
Refinement SpaceREAL
Refinement Protocolrigid body
DetailsProtocol: rigid body
PDB Entry ID3CF3
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1932.xml (7.8 KB)
Map dataemd_1932.map.gz (147 KB)
Imagesemd-1932.png (121.7 KB)
emd_1932.png (105.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1932
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.7 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 1.4 MB