+Open data
-Basic information
Entry | Database: PDB / ID: 6lrs | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of RbcL8-RbcS4 from Anabaena sp. PCC 7120 | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | LYASE / RuBisCO / Chaperone / Raf1 / PHOTOSYNTHESIS | ||||||||||||||||||
Function / homology | Function and homology information carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Nostoc sp. (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å | ||||||||||||||||||
Authors | Xia, L.Y. / Jiang, Y.L. / Kong, W.W. / Sun, H. / Li, W.F. / Chen, Y. / Zhou, C.Z. | ||||||||||||||||||
Funding support | China, 5items
| ||||||||||||||||||
Citation | Journal: Nat Plants / Year: 2020 Title: Molecular basis for the assembly of RuBisCO assisted by the chaperone Raf1. Authors: Ling-Yun Xia / Yong-Liang Jiang / Wen-Wen Kong / Hui Sun / Wei-Fang Li / Yuxing Chen / Cong-Zhao Zhou / Abstract: The folding and assembly of RuBisCO, the most abundant enzyme in nature, needs a series of chaperones, including the RuBisCO accumulation factor Raf1, which is highly conserved in cyanobacteria and ...The folding and assembly of RuBisCO, the most abundant enzyme in nature, needs a series of chaperones, including the RuBisCO accumulation factor Raf1, which is highly conserved in cyanobacteria and plants. Here, we report the crystal structures of Raf1 from cyanobacteria Anabaena sp. PCC 7120 and its complex with RuBisCO large subunit RbcL. Structural analyses and biochemical assays reveal that each Raf1 dimer captures an RbcL dimer, with the C-terminal tail inserting into the catalytic pocket, and further mediates the assembly of RbcL dimers to form the octameric core of RuBisCO. Furthermore, the cryo-electron microscopy structures of the RbcL-Raf1-RbcS assembly intermediates enable us to see a dynamic assembly process from RbcLRaf1 to the holoenzyme RbcLRbcS. In vitro assays also indicate that Raf1 can attenuate and reverse CcmM-mediated cyanobacterial RuBisCO condensation. Combined with previous findings, we propose a putative model for the assembly of cyanobacterial RuBisCO coordinated by the chaperone Raf1. | ||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6lrs.cif.gz | 639.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6lrs.ent.gz | 546.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lrs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lrs_validation.pdf.gz | 1022.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6lrs_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6lrs_validation.xml.gz | 101.5 KB | Display | |
Data in CIF | 6lrs_validation.cif.gz | 154.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/6lrs ftp://data.pdbj.org/pub/pdb/validation_reports/lr/6lrs | HTTPS FTP |
-Related structure data
Related structure data | 0960MC 0959C 0961C 0962C 6kkmC 6kknC 6lrrC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 12840.725 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: cbbS, rbcS, alr1526 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P06514, ribulose-bisphosphate carboxylase #2: Protein | Mass: 53112.125 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) Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: cbbL, rbc, rbcA, rbcL, alr1524 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P00879, ribulose-bisphosphate carboxylase |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The complex of RbcL8-RbcS4 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.9 MDa / Experimental value: NO |
Source (natural) | Organism: Nostoc sp. PCC 7120 (bacteria) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: DIFFRACTION |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | ||||||||||||||||||
3D reconstruction | Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 340899 / Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||
Atomic model building | PDB-ID: 1RBL |