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- PDB-6z1f: CryoEM structure of Rubisco Activase with its substrate Rubisco f... -
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Basic information
Entry | Database: PDB / ID: 6z1f | ||||||
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Title | CryoEM structure of Rubisco Activase with its substrate Rubisco from Nostoc sp. (strain PCC7120) | ||||||
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![]() | CHAPERONE / AAA+ / beta barrel | ||||||
Function / homology | ![]() carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | ||||||
![]() | Wang, H. / Bracher, A. / Flecken, M. / Popilka, L. / Hartl, F.U. / Hayer-Hartl, M. | ||||||
![]() | ![]() Title: Dual Functions of a Rubisco Activase in Metabolic Repair and Recruitment to Carboxysomes. Authors: Mirkko Flecken / Huping Wang / Leonhard Popilka / F Ulrich Hartl / Andreas Bracher / Manajit Hayer-Hartl / ![]() Abstract: Rubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone ...Rubisco, the key enzyme of CO fixation in photosynthesis, is prone to inactivation by inhibitory sugar phosphates. Inhibited Rubisco undergoes conformational repair by the hexameric AAA+ chaperone Rubisco activase (Rca) in a process that is not well understood. Here, we performed a structural and mechanistic analysis of cyanobacterial Rca, a close homolog of plant Rca. In the Rca:Rubisco complex, Rca is positioned over the Rubisco catalytic site under repair and pulls the N-terminal tail of the large Rubisco subunit (RbcL) into the hexamer pore. Simultaneous displacement of the C terminus of the adjacent RbcL opens the catalytic site for inhibitor release. An alternative interaction of Rca with Rubisco is mediated by C-terminal domains that resemble the small Rubisco subunit. These domains, together with the N-terminal AAA+ hexamer, ensure that Rca is packaged with Rubisco into carboxysomes. The cyanobacterial Rca is a dual-purpose protein with functions in Rubisco repair and carboxysome organization. | ||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 1004.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11028MC ![]() 6hasC ![]() 6z1dC ![]() 6z1eC ![]() 6z1gC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Ribulose bisphosphate carboxylase ... , 2 types, 16 molecules ABCDEFGHIJKLMNOP
#2: Protein | Mass: 53155.125 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cbbL, rbc, rbcA, rbcL, alr1524 / Plasmid: pET11a-NosGroSEL-H6ubi-NosLS / Cell line (production host): STAR / Production host: ![]() ![]() References: UniProt: P00879, ribulose-bisphosphate carboxylase #3: Protein | Mass: 12840.725 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: cbbS, rbcS, alr1526 / Plasmid: pET11a-NosGroSEL-H6ubi-NosLS / Cell line (production host): STAR / Production host: ![]() ![]() References: UniProt: P06514, ribulose-bisphosphate carboxylase |
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-Protein / Sugars , 2 types, 13 molecules 123456![](data/chem/img/CAP.gif)
![](data/chem/img/CAP.gif)
#1: Protein | Mass: 32773.316 Da / Num. of mol.: 6 / Fragment: AAA+ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: rca, alr1533 / Plasmid: pHUE / Cell line (production host): pBAD33-EcGroSEL / Production host: ![]() ![]() #7: Sugar | ChemComp-CAP / |
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-Non-polymers , 3 types, 18 molecules ![](data/chem/img/ADP.gif)
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![](data/chem/img/MG.gif)
![](data/chem/img/AGS.gif)
![](data/chem/img/MG.gif)
#4: Chemical | ChemComp-ADP / | ||
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#5: Chemical | ChemComp-AGS / #6: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: NosRubisco (1 uM) was incubated with NaHCO3 (10 mM) at 298 K for 10 min followed by addition of CABP (8 uM). CABP-inhibited NosRubisco (0.5 uM) was then incubated with NosRcaDC (10 uM) in ...Details: NosRubisco (1 uM) was incubated with NaHCO3 (10 mM) at 298 K for 10 min followed by addition of CABP (8 uM). CABP-inhibited NosRubisco (0.5 uM) was then incubated with NosRcaDC (10 uM) in the presence of ATP (2 mM) for 10 s, followed by the addition of ATP-gammaS (2 mM), and incubated at 298 K for another 10 min before preparing the cryo-grids. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 2.8 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9042 / Details: 31 frames per image |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 519151 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21149 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL |