[English] 日本語
Yorodumi- PDB-6z1f: CryoEM structure of Rubisco Activase with its substrate Rubisco f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z1f | ||||||
---|---|---|---|---|---|---|---|
Title | CryoEM structure of Rubisco Activase with its substrate Rubisco from Nostoc sp. (strain PCC7120) | ||||||
Components |
| ||||||
Keywords | CHAPERONE / AAA+ / beta barrel | ||||||
Function / homology | Function and homology information 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 | Nostoc sp. (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | ||||||
Authors | Wang, H. / Bracher, A. / Flecken, M. / Popilka, L. / Hartl, F.U. / Hayer-Hartl, M. | ||||||
Citation | Journal: Cell / Year: 2020 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6z1f.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6z1f.ent.gz | 1004.8 KB | Display | PDB format |
PDBx/mmJSON format | 6z1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z1f_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6z1f_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6z1f_validation.xml.gz | 158.9 KB | Display | |
Data in CIF | 6z1f_validation.cif.gz | 238 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/6z1f ftp://data.pdbj.org/pub/pdb/validation_reports/z1/6z1f | HTTPS FTP |
-Related structure data
Related structure data | 11028MC 6hasC 6z1dC 6z1eC 6z1gC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Gene: cbbL, rbc, rbcA, rbcL, alr1524 / Plasmid: pET11a-NosGroSEL-H6ubi-NosLS / Cell line (production host): STAR / Production host: Escherichia coli BL21 (bacteria) 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.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Gene: cbbS, rbcS, alr1526 / Plasmid: pET11a-NosGroSEL-H6ubi-NosLS / Cell line (production host): STAR / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P06514, ribulose-bisphosphate carboxylase |
---|
-Protein / Sugars , 2 types, 13 molecules 123456
#1: Protein | Mass: 32773.316 Da / Num. of mol.: 6 / Fragment: AAA+ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Gene: rca, alr1533 / Plasmid: pHUE / Cell line (production host): pBAD33-EcGroSEL / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P58555 #7: Sugar | ChemComp-CAP / |
---|
-Non-polymers , 3 types, 18 molecules
#4: Chemical | ChemComp-ADP / | ||
---|---|---|---|
#5: Chemical | ChemComp-AGS / #6: Chemical | ChemComp-MG / |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 8.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
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 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |