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- PDB-3zuh: Negative stain EM Map of the AAA protein CbbX, a red-type Rubisco... -

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Basic information

Entry
Database: PDB / ID: 3zuh
TitleNegative stain EM Map of the AAA protein CbbX, a red-type Rubisco activase from R. sphaeroides
ComponentsPROTEIN CBBX
KeywordsATP BINDING PROTEIN / AAA+ PROTEIN
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
CbxX/CfxQ, monofunctional / CbxX/CfxQ / CbbX, AAA lid domain / AAA lid domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RIBULOSE-1,5-DIPHOSPHATE / Protein CbbX
Similarity search - Component
Biological speciesRHODOBACTER SPHAEROIDES (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 21 Å
AuthorsMueller-Cajar, O. / Stotz, M. / Wendler, P. / Hartl, F.U. / Bracher, A. / Hayer-Hartl, M.
CitationJournal: Nature / Year: 2011
Title: Structure and function of the AAA+ protein CbbX, a red-type Rubisco activase.
Authors: Oliver Mueller-Cajar / Mathias Stotz / Petra Wendler / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl /
Abstract: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the fixation of atmospheric CO(2) in photosynthesis, but tends to form inactive complexes with its substrate ribulose 1,5- ...Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyses the fixation of atmospheric CO(2) in photosynthesis, but tends to form inactive complexes with its substrate ribulose 1,5-bisphosphate (RuBP). In plants, Rubisco is reactivated by the AAA(+) (ATPases associated with various cellular activities) protein Rubisco activase (Rca), but no such protein is known for the Rubisco of red algae. Here we identify the protein CbbX as an activase of red-type Rubisco. The 3.0-Å crystal structure of unassembled CbbX from Rhodobacter sphaeroides revealed an AAA(+) protein architecture. Electron microscopy and biochemical analysis showed that ATP and RuBP must bind to convert CbbX into functionally active, hexameric rings. The CbbX ATPase is strongly stimulated by RuBP and Rubisco. Mutational analysis suggests that CbbX functions by transiently pulling the carboxy-terminal peptide of the Rubisco large subunit into the hexamer pore, resulting in the release of the inhibitory RuBP. Understanding Rubisco activation may facilitate efforts to improve CO(2) uptake and biomass production by photosynthetic organisms.
History
DepositionJul 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Aug 27, 2014Group: Other
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Structure visualization

Movie
  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-1932
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Assembly

Deposited unit
A: PROTEIN CBBX
B: PROTEIN CBBX
C: PROTEIN CBBX
D: PROTEIN CBBX
E: PROTEIN CBBX
F: PROTEIN CBBX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,10218
Polymers195,6786
Non-polymers4,42412
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
PROTEIN CBBX / RUBISCO ACTIVASE CBBX


Mass: 32612.963 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN IS BOUND TO RIBULOSE-1,5-BISPHOSPHATE / Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95648
#2: Sugar
ChemComp-RUB / RIBULOSE-1,5-DIPHOSPHATE / Ribulose 1,5-bisphosphate


Type: saccharideCarbohydrate / Mass: 310.090 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C5H12O11P2
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Nonpolymer detailsADENOSINE-5'-DIPHOSPHATE (ADP): MODELLED FROM P97 D2 (PDB 3CF3)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PROTEIN CBBX / Type: COMPLEX
Buffer solutionName: 20 MM TRIS PH 8.0, 50 MM NACL, 5MM MGCL2, 1MM RIBULOSE-1,5- BISPHOSPHATE, 1MM ATP/ATPGAMMAS
pH: 8
Details: 20 MM TRIS PH 8.0, 50 MM NACL, 5MM MGCL2, 1MM RIBULOSE-1,5- BISPHOSPHATE, 1MM ATP/ATPGAMMAS
SpecimenConc.: 0.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: NO
EM stainingType: NEGATIVE / Material: uranyl acetate
Specimen supportDetails: CARBON

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 12 / Date: Nov 19, 2010
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 90600 X / Calibrated magnification: 90600 X / Nominal defocus max: 1800 nm / Nominal defocus min: 260 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (2k x 2k)
Image scansNum. digital images: 12
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1IMAGIC3D reconstruction
2MRC IMAGE PROCESSING PACKAGE3D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: PHASE FLIPPING, EACH PARTICLE
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionMethod: ANGULAR RECONSTITUTION / Resolution: 21 Å / Num. of particles: 245 / Nominal pixel size: 3.308 Å / Actual pixel size: 3.308 Å
Details: MODULE 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.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--MANUAL
Atomic model buildingPDB-ID: 3SYL

3syl

RefinementHighest resolution: 21 Å
Refinement stepCycle: LAST / Highest resolution: 21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13614 0 270 0 13884

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