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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

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#1: Depositted structure unit, Made by Jmol

#2: Superimposing with EM 3D map: EMDB-1932, Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3zuh
TitleNEGATIVE STAIN EM MAP OF THE AAA PROTEIN CBBX, A RED-TYPE RUBISCO ACTIVASE FROM R. SPHAEROIDES
DescriptorPROTEIN CBBX
KeywordsATP BINDING PROTEIN, AAA+ PROTEIN
AuthorsMueller-Cajar, O., Stotz, M., Wendler, P., Hartl, F.U., Bracher, A., Hayer-Hartl, M.
DateDeposition: 2011-07-19, Release: 2011-11-09
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Nonpolymer detailsADENOSINE-5'-DIPHOSPHATE (ADP): MODELLED FROM P97 D2 (PDB 3CF3)
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Made by Jmol

#2: Superimposing with EM 3D map: EMDB-1932, Made by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
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EMDB-1932

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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
Components
ID 1 : RUBISCO ACTIVASE CBBX
Image
DescriptionPROTEIN CBBX
Typepolypeptide(L)
Formula weight32613.229 Da
Number of molecules6
ID1
DetailsTHE PROTEIN IS BOUND TO RIBULOSE-1,5-BISPHOSPHATE
SourceMethod: Isolated from a genetically manipulated source
Gene: ID:1063, RHODOBACTER SPHAEROIDES
Host: ID:469008, ESCHERICHIA COLI

, BL21(DE3), PHUE, PLASMID
LinksUniProt: P95648, Sequence view
ID 2 : SUGAR (RIBULOSE-1,5-DIPHOSPHATE)
Image
DescriptionSUGAR (RIBULOSE-1,5-DIPHOSPHATE)
Typenon-polymer
Formula weight310.091 Da
Number of molecules6
ID2
SourceMethod: Isolated from a genetically manipulated source
ID 3 : ADENOSINE-5'-DIPHOSPHATE
Image
DescriptionADENOSINE-5'-DIPHOSPHATE
Typenon-polymer
Formula weight427.203 Da
Number of molecules6
ID3
SourceMethod: Obtained synthetically
Sample
Assembly
Aggregation statePARTICLE
NamePROTEIN CBBX
Buffer
Name20 MM TRIS PH 8.0, 50 MM NACL, 5MM MGCL2, 1MM RIBULOSE-1,5- BISPHOSPHATE, 1MM ATP/ATPGAMMAS
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeNEGATIVE STAIN
Sample preparation
pH8.0
Sample concentration0.07 mg/ml
Sample support
DetailsCARBON
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TECNAI 12
Date2010-11-19
Electron gun
Electron sourceLAB6
Accelerating voltage120 kV
Electron dose20 e/A**2
Illumination modeLOW DOSE
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 90600 X, Nominal: 90600 X
CsNominal: 2.0 mm
Nominal defocusMax: 1800 nm, Min: 260 nm
Detector
TypeEAGLE 2K CCD
Image scans
Number digital images12
Processing
2D projection selection
Number of particles245
Software nameMRC, IMAGIC, SPIDER
Single particle entity
Symmetry typeMIXED SYMMETRY
3D reconstruction
Actual pixel size3.308 A/pix
CTF correction methodPHASE FLIPPING, EACH PARTICLE
DetailsMODULE CONSISTING OF CHAIN A (204-296) AND CHAIN B (8-203) AS FOUND IN PDB 3SYL WAS MODELLED ONTO D2 P97 OF PDB 3CF3. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1932.
MethodANGULAR RECONSTITUTION
Nominal pixel size3.308 A/pix
Resolution21 A
3D fitting
MethodRIGID BODY
Refinement ProtocolMANUAL
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID3SYL
Refine
Refine idELECTRON MICROSCOPY
Ls d res high21.00 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high21.00
Total atoms13884
Ligand atoms270
Protein atoms13614
Download
PDB format
Allpdb3zuh.ent.gz
pdb3zuh.ent (uncompressed file)
Header onlypdb3zuh.ent.gz
mmCIF format
mmCIF3zuh.cif.gz
XML format
All3zuh.xml.gz
No-atom3zuh-noatom.xml.gz
Ext-atom3zuh-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5 MB