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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

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
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
Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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