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- PDB-8ilb: The complexes of RbcL, AtRaf1 and AtBSD2 (LFB) -

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Basic information

Entry
Database: PDB / ID: 8ilb
TitleThe complexes of RbcL, AtRaf1 and AtBSD2 (LFB)
Components
  • Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
  • Ribulose bisphosphate carboxylase large chain
  • Rubisco accumulation factor 1.2, chloroplastic
KeywordsLYASE/CHAPERONE / RUBISCO ASSEMBL INTERMIDATES / COMPLEX / CHAPERONE / LYASE-CHAPERONE complex
Function / homology
Function and homology information


ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone complex / chloroplast stroma / chaperone-mediated protein folding / protein folding chaperone ...ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone complex / chloroplast stroma / chaperone-mediated protein folding / protein folding chaperone / chloroplast / monooxygenase activity / magnesium ion binding / metal ion binding / cytosol
Similarity search - Function
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 / Heat shock protein DnaJ, cysteine-rich domain superfamily / Ribulose bisphosphate carboxylase large subunit, type I / Ribulose bisphosphate carboxylase, large chain, active site ...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 / Heat shock protein DnaJ, cysteine-rich domain superfamily / 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
Ribulose bisphosphate carboxylase large chain / Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic / Rubisco accumulation factor 1.2, chloroplastic
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 6301 (bacteria)
Arabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWang, R. / Song, H. / Zhang, W. / Wang, N. / Zhang, S. / Shao, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol Plant / Year: 2023
Title: Structural insights into the functions of Raf1 and Bsd2 in hexadecameric Rubisco assembly.
Authors: Ran Wang / Hui Song / Wenjuan Zhang / Ning Wang / Shijia Zhang / Ruiqi Shao / Cuimin Liu /
Abstract: Hexadecameric form I Rubisco, which consisting consists of eight large (RbcL) and eight small (RbcS) subunits, is the most abundant enzyme on earth. Extensive efforts to engineer an improved Rubisco ...Hexadecameric form I Rubisco, which consisting consists of eight large (RbcL) and eight small (RbcS) subunits, is the most abundant enzyme on earth. Extensive efforts to engineer an improved Rubisco to speed up its catalytic efficiency and ultimately increase agricultural productivity. However, difficulties with correct folding and assembly in foreign hosts or in vitro have hampered the genetic manipulation of hexadecameric Rubisco. In this study, we reconstituted Synechococcus sp. PCC6301 Rubisco in vitro using the chaperonin system and assembly factors from cyanobacteria and Arabidopsis thaliana (At). Rubisco holoenzyme was produced in the presence of cyanobacterial Rubisco accumulation factor 1 (Raf1) alone or both AtRaf1 and bundle-sheath defective-2 (AtBsd2) from Arabidopsis. RbcL released from GroEL is assembly capable in the presence of ATP, and AtBsd2 functions downstream of AtRaf1. Cryo-EM structures of RbcL-AtRaf1, RbcL-AtRaf1-AtBsd2, and RbcL revealed that the interactions between RbcL and AtRaf1 are looser than those between prokaryotic RbcL and Raf1, with AtRaf1 tilting 7° farther away from RbcL. AtBsd2 stabilizes the flexible regions of RbcL, including the N and C termini, the 60s loop, and loop 6. Using these data, combined with previous findings, we propose the possible biogenesis pathways of prokaryotic and eukaryotic Rubisco.
History
DepositionMar 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
E: Rubisco accumulation factor 1.2, chloroplastic
F: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
G: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
H: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
I: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
J: Ribulose bisphosphate carboxylase large chain
K: Ribulose bisphosphate carboxylase large chain
L: Ribulose bisphosphate carboxylase large chain
M: Ribulose bisphosphate carboxylase large chain
N: Rubisco accumulation factor 1.2, chloroplastic
O: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
P: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
Q: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
R: Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic


Theoretical massNumber of molelcules
Total (without water)574,44218
Polymers574,44218
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 52516.605 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 6301 (bacteria)
Gene: cbbL, rbcA, rbcL, syc0130_c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00880, ribulose-bisphosphate carboxylase
#2: Protein Rubisco accumulation factor 1.2, chloroplastic


Mass: 43732.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RAF1.2, At3g04550, F7O18.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SR19
#3: Protein
Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic / AtBSD2


Mass: 8355.468 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BSD2, At3g47650, F1P2.200 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SN73

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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: Rubisco assembly intermidate complex with Syn6301RbcL, AtRaf1 and AtBsd2
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 233489 / Symmetry type: POINT

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