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- PDB-3zw6: MODEL OF HEXAMERIC AAA DOMAIN ARRANGEMENT OF GREEN-TYPE RUBISCO A... -

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Basic information

Entry
Database: PDB / ID: 3zw6
TitleMODEL OF HEXAMERIC AAA DOMAIN ARRANGEMENT OF GREEN-TYPE RUBISCO ACTIVASE FROM TOBACCO.
ComponentsRIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE ACTIVASE 1, CHLOROPLASTIC
KeywordsPHOTOSYNTHESIS / NEGATIVE STAIN EM
Function / homology
Function and homology information


ribulose-1,5-bisphosphate carboxylase/oxygenase activator activity / chloroplast stroma / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Ribulose bisphosphate carboxylase/oxygenase activase-like / : / Ribulose bisphosphate carboxylase/oxygenase activase, AAA, helical / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ribulose bisphosphate carboxylase/oxygenase activase 1, chloroplastic
Similarity search - Component
Biological speciesNICOTIANA TABACUM (common tobacco)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / Resolution: 20 Å
AuthorsStotz, M. / Mueller-Cajar, O. / Ciniawsky, S. / Wendler, P. / Hartl, F.U. / Bracher, A. / Hayer-Hartl, M.
CitationJournal: Nat Struct Mol Biol / Year: 2011
Title: Structure of green-type Rubisco activase from tobacco.
Authors: Mathias Stotz / Oliver Mueller-Cajar / Susanne Ciniawsky / Petra Wendler / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl /
Abstract: Rubisco, the enzyme that catalyzes the fixation of atmospheric CO(2) in photosynthesis, is subject to inactivation by inhibitory sugar phosphates. Here we report the 2.95-Å crystal structure of ...Rubisco, the enzyme that catalyzes the fixation of atmospheric CO(2) in photosynthesis, is subject to inactivation by inhibitory sugar phosphates. Here we report the 2.95-Å crystal structure of Nicotiana tabacum Rubisco activase (Rca), the enzyme that facilitates the removal of these inhibitors. Rca from tobacco has a classical AAA(+)-protein domain architecture. Although Rca populates a range of oligomeric states when in solution, it forms a helical arrangement with six subunits per turn when in the crystal. However, negative-stain electron microscopy of the active mutant R294V suggests that Rca functions as a hexamer. The residues determining species specificity for Rubisco are located in a helical insertion of the C-terminal domain and probably function in conjunction with the N-domain in Rubisco recognition. Loop segments exposed toward the central pore of the hexamer are required for the ATP-dependent remodeling of Rubisco, resulting in the release of inhibitory sugar.
History
DepositionJul 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3Oct 23, 2019Group: Data collection / Derived calculations / Other / Category: cell / struct_conn / Item: _cell.Z_PDB / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 30, 2019Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.5May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-1940
  • Imaged by UCSF Chimera
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Assembly

Deposited unit
A: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE ACTIVASE 1, CHLOROPLASTIC
B: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE ACTIVASE 1, CHLOROPLASTIC
C: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE ACTIVASE 1, CHLOROPLASTIC
D: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE ACTIVASE 1, CHLOROPLASTIC
E: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE ACTIVASE 1, CHLOROPLASTIC
F: RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE ACTIVASE 1, CHLOROPLASTIC


Theoretical massNumber of molelcules
Total (without water)197,1416
Polymers197,1416
Non-polymers00
Water00
1


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

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Components

#1: Protein
RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE ACTIVASE 1, CHLOROPLASTIC / RA 1 / RUBISCO ACTIVASE 1


Mass: 32856.801 Da / Num. of mol.: 6 / Fragment: AAA ATPASE DOMAIN, RESIDUES 127-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NICOTIANA TABACUM (common tobacco) / Plasmid: PHUENTRCA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q40460

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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: NICOTIANA TABACUM RUBISCO ACTIVASE (R294V) / Type: COMPLEX / Details: THE PROTEIN FOR EM CARRIES A R294V MUTATION
Buffer solutionName: 20MM TRIS-HCL, 50MM NACL, 2MM MGCL2,1MM ATPGAMMAS / pH: 8 / Details: 20MM TRIS-HCL, 50MM NACL, 2MM MGCL2,1MM ATPGAMMAS
SpecimenConc.: 0.04 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: Jun 22, 2011
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 950 nm / Nominal defocus min: 470 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (2k x 2k)
Image scansNum. digital images: 11
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2IMAGIC3D reconstruction
3MRC IMAGE PROCESSING PACKAGE3D reconstruction
4SPIDER3D reconstruction
CTF correctionDetails: PHASE FLIPPING, EACH PARTICLE
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionMethod: ANGULAR RECONSTITUTION / Resolution: 20 Å / Num. of particles: 599 / Nominal pixel size: 3.308 Å / Actual pixel size: 3.308 Å
Details: A MODULE OF ALPHA HELICAL DOMAIN AND ALPHA-BETA DOMAIN OF THE NEIGHBOURING SUBUNIT WAS OVERLAID WITH THE P97 D2 (3CF3) STRUCTURE AND THE HEXAMER WAS FITTED INTO THE EM MAP SUBMISSION BASED ...Details: A MODULE OF ALPHA HELICAL DOMAIN AND ALPHA-BETA DOMAIN OF THE NEIGHBOURING SUBUNIT WAS OVERLAID WITH THE P97 D2 (3CF3) STRUCTURE AND THE HEXAMER WAS FITTED INTO THE EM MAP SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1940. (DEPOSITION ID: 10169).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: LOCAL MINIMISATION, FIT IN MAP / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 3T15

3t15


Accession code: 3T15 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 20 Å
Refinement stepCycle: LAST / Highest resolution: 20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12492 0 0 0 12492

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