7T1C

Crystal structure of RUBISCO from Sulfurivirga caldicuralii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural plasticity enables evolution and innovation of RuBisCO assemblies.

Liu, A.K.Pereira, J.H.Kehl, A.J.Rosenberg, D.J.Orr, D.J.Chu, S.K.S.Banda, D.M.Hammel, M.Adams, P.D.Siegel, J.B.Shih, P.M.

(2022) Sci Adv 8: eadc9440-eadc9440

  • DOI: https://doi.org/10.1126/sciadv.adc9440
  • Primary Citation of Related Structures:  
    7T1C, 7T1J

  • PubMed Abstract: 

    Oligomerization is a core structural feature that defines the form and function of many proteins. Most proteins form molecular complexes; however, there remains a dearth of diversity-driven structural studies investigating the evolutionary trajectory of these assemblies. Ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is one such enzyme that adopts multiple assemblies, although the origins and distribution of its different oligomeric states remain cryptic. Here, we retrace the evolution of ancestral and extant form II RuBisCOs, revealing a complex and diverse history of oligomerization. We structurally characterize a newly discovered tetrameric RuBisCO, elucidating how solvent-exposed surfaces can readily adopt new interactions to interconvert or give rise to new oligomeric states. We further use these principles to engineer and demonstrate how changes in oligomerization can be mediated by relatively few mutations. Our findings yield insight into how structural plasticity may give rise to new oligomeric states.


  • Organizational Affiliation

    Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribulose-bisphosphate carboxylase466Sulfurivirga caldicuraliiMutation(s): 0 
Gene Names: SAMN05443662_0203
EC: 4.1.1.39
UniProt
Find proteins for A0A1N6DK16 (Sulfurivirga caldicuralii)
Explore A0A1N6DK16 
Go to UniProtKB:  A0A1N6DK16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1N6DK16
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.056α = 90
b = 133.056β = 90
c = 112.456γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description