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- PDB-7xsd: Cryo-EM structure of RuBisCO assembly intermediate RbcL8Raf18RbcX16 -

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Basic information

Entry
Database: PDB / ID: 7xsd
TitleCryo-EM structure of RuBisCO assembly intermediate RbcL8Raf18RbcX16
Components
  • Ribulose bisphosphate carboxylase large chain
  • RuBisCO accumulation factor 1
  • RuBisCO chaperone RbcX
KeywordsPHOTOSYNTHESIS / RuBisCO intermediate
Function / homology
Function and homology information


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
Rubisco accumulation factor 1, cyanobacterial / Rubisco accumulation factor 1 / Rubisco accumulation factor 1, helix turn helix domain / Rubisco accumulation factor 1, C-terminal / Rubisco accumulation factor 1, alpha helical domain / Rubisco Assembly chaperone C-terminal domain / Rubisco accumulation factor 1 alpha helical domain / Rubisco accumulation factor 1 helix turn helix domain / Chaperonin-like RbcX superfamily / RbcX protein ...Rubisco accumulation factor 1, cyanobacterial / Rubisco accumulation factor 1 / Rubisco accumulation factor 1, helix turn helix domain / Rubisco accumulation factor 1, C-terminal / Rubisco accumulation factor 1, alpha helical domain / Rubisco Assembly chaperone C-terminal domain / Rubisco accumulation factor 1 alpha helical domain / Rubisco accumulation factor 1 helix turn helix domain / Chaperonin-like RbcX superfamily / RbcX protein / Chaperonin-like RbcX / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain
Similarity search - Domain/homology
RuBisCO chaperone RbcX / Ribulose bisphosphate carboxylase large chain / RuBisCO accumulation factor 1
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsJiang, Y.L. / Xia, L.Y. / Zhou, C.Z.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDA24020302 and XDB37020301 China
National Natural Science Foundation of China (NSFC)32171198 China
Ministry of Science and Technology (MoST, China)2016YFA0400900 China
CitationJournal: Cell Discov / Year: 2022
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
DepositionMay 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
5: RuBisCO chaperone RbcX
6: RuBisCO chaperone RbcX
7: RuBisCO chaperone RbcX
8: RuBisCO chaperone RbcX
O: RuBisCO accumulation factor 1
P: RuBisCO accumulation factor 1
G: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase large chain
1: RuBisCO chaperone RbcX
2: RuBisCO chaperone RbcX
3: RuBisCO chaperone RbcX
4: RuBisCO chaperone RbcX
M: RuBisCO accumulation factor 1
N: RuBisCO accumulation factor 1
E: Ribulose bisphosphate carboxylase large chain
F: Ribulose bisphosphate carboxylase large chain
I: RuBisCO accumulation factor 1
J: RuBisCO accumulation factor 1
Q: RuBisCO chaperone RbcX
R: RuBisCO chaperone RbcX
S: RuBisCO chaperone RbcX
T: RuBisCO chaperone RbcX
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
K: RuBisCO accumulation factor 1
L: RuBisCO accumulation factor 1
U: RuBisCO chaperone RbcX
V: RuBisCO chaperone RbcX
W: RuBisCO chaperone RbcX
X: RuBisCO chaperone RbcX
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain


Theoretical massNumber of molelcules
Total (without water)996,66932
Polymers996,66932
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
RuBisCO chaperone RbcX


Mass: 15208.165 Da / Num. of mol.: 16
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: rbcX, alr1525 / Production host: Escherichia coli (E. coli) / References: UniProt: O86418
#2: Protein
RuBisCO accumulation factor 1 / Raf1


Mass: 41055.113 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: all5250 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YLP6
#3: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


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 (E. coli)
References: UniProt: P00879, ribulose-bisphosphate carboxylase

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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: The termary complex of RbcL-Raf1-RbcX / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.05 MDa / Experimental value: YES
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8 / Details: 50 mM Tris-HCl, pH 8.0, 20 mM NaCl, 5 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: 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
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54260 / Symmetry type: POINT

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