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- PDB-7xsd: Cryo-EM structure of RuBisCO assembly intermediate RbcL8Raf18RbcX16 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xsd | ||||||||||||
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Title | Cryo-EM structure of RuBisCO assembly intermediate RbcL8Raf18RbcX16 | ||||||||||||
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![]() | PHOTOSYNTHESIS / RuBisCO intermediate | ||||||||||||
Function / homology | ![]() ribulose bisphosphate carboxylase complex assembly / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone / photosynthesis / monooxygenase activity ...ribulose bisphosphate carboxylase complex assembly / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone / photosynthesis / monooxygenase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Jiang, Y.L. / Xia, L.Y. / Zhou, C.Z. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into cyanobacterial RuBisCO assembly coordinated by two chaperones Raf1 and RbcX. Authors: Qiong Li / Yong-Liang Jiang / Ling-Yun Xia / Yuxing Chen / Cong-Zhao Zhou / ![]() Abstract: RuBisCO is the most abundant enzyme in nature, catalyzing the fixation of CO in photosynthesis. Its common form consists of eight RbcL and eight RbcS subunits, the assembly of which requires a series ...RuBisCO is the most abundant enzyme in nature, catalyzing the fixation of CO in photosynthesis. Its common form consists of eight RbcL and eight RbcS subunits, the assembly of which requires a series of chaperones that include RbcX and RuBisCO accumulation factor 1 (Raf1). To understand how these RuBisCO-specific chaperones function during cyanobacterial RbcLRbcS (LS) holoenzyme formation, we solved a 3.3-Å cryo-electron microscopy structure of a 32-subunit RbcLRaf1RbcX (LFX) assembly intermediate from Anabaena sp. PCC 7120. Comparison to the previously resolved LF and LX structures together with biochemical assays revealed that the LFX complex forms a rather dynamic structural intermediate, favoring RbcS displacement of Raf1 and RbcX. In vitro assays further demonstrated that both Raf1 and RbcX function to regulate RuBisCO condensate formation by restricting CcmM35 binding to the stably assembled LS holoenzymes. Combined with previous findings, we propose a model on how Raf1 and RbcX work in concert to facilitate, and regulate, cyanobacterial RuBisCO assembly as well as disassembly of RuBisCO condensates. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 893.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 165.8 KB | Display | |
Data in CIF | ![]() | 250.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33524MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 15208.165 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: rbcX, alr1525 / Production host: ![]() ![]() #2: Protein | Mass: 41055.113 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all5250 / Production host: ![]() ![]() #3: Protein | Mass: 53112.125 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: cbbL, rbc, rbcA, rbcL, alr1524 / Production host: ![]() ![]() References: UniProt: P00879, ribulose-bisphosphate carboxylase |
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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
Component | Name: The termary complex of RbcL-Raf1-RbcX / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 1.05 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 / Details: 50 mM Tris-HCl, pH 8.0, 20 mM NaCl, 5 mM MgCl2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54260 / Symmetry type: POINT |