8ILM

The cryo-EM structure of eight Rubisco large subunits (RbcL), two Arabidopsis thaliana Rubisco accumulation factors 1 (AtRaf1), and seven Arabidopsis thaliana Bundle Sheath Defective 2 (AtBSD2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the functions of Raf1 and Bsd2 in hexadecameric Rubisco assembly.

Wang, R.Song, H.Zhang, W.Wang, N.Zhang, S.Shao, R.Liu, C.

(2023) Mol Plant 16: 1927-1936

  • DOI: https://doi.org/10.1016/j.molp.2023.10.011
  • Primary Citation of Related Structures:  
    8ILB, 8ILM, 8IO2, 8IOJ, 8IOL

  • PubMed 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 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 8 -AtRaf1 8 , RbcL 8 -AtRaf1 4 -AtBsd2 8 , and RbcL 8 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.


  • Organizational Affiliation

    State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose bisphosphate carboxylase large chain
A, B, F, G, H
A, B, F, G, H, I, J, K
472Synechococcus elongatus PCC 6301Mutation(s): 0 
Gene Names: cbbLrbcArbcLsyc0130_c
EC: 4.1.1.39
UniProt
Find proteins for P00880 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1))
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Go to UniProtKB:  P00880
Entity Groups  
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UniProt GroupP00880
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic
C, L, M, N, O
C, L, M, N, O, P, Q
81Arabidopsis thalianaMutation(s): 0 
Gene Names: BSD2At3g47650F1P2.200
UniProt
Find proteins for Q9SN73 (Arabidopsis thaliana)
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Go to UniProtKB:  Q9SN73
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UniProt GroupQ9SN73
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Rubisco accumulation factor 1.2, chloroplastic
D, E, R, S
389Arabidopsis thalianaMutation(s): 0 
Gene Names: RAF1.2At3g04550F7O18.2
UniProt
Find proteins for Q9SR19 (Arabidopsis thaliana)
Explore Q9SR19 
Go to UniProtKB:  Q9SR19
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UniProt GroupQ9SR19
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary