Structural basis of a superoxide dismutase from a tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1.

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.198 

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Structure of a superoxide dismutase from a tardigrade: Ramazzottius varieornatus strain YOKOZUNA-1.

Sim, K.S.Inoue, T.

(2023) Acta Crystallogr F Struct Biol Commun 79: 169-179

  • DOI: https://doi.org/10.1107/S2053230X2300523X
  • Primary Citation of Related Structures:  
    7YPP, 7YPR

  • PubMed Abstract: 

    Superoxide dismutase (SOD) is an essential and ubiquitous antioxidant protein that is widely present in biological systems. The anhydrobiotic tardigrades are some of the toughest micro-animals. They have an expanded set of genes for antioxidant proteins such as SODs. These proteins are thought to play an essential role in oxidative stress resistance in critical situations such as desiccation, although their functions at the molecular level have yet to be explored. Here, crystal structures of a copper/zinc-containing SOD (RvSOD15) from an anhydrobiotic tardigrade, Ramazzottius varieornatus strain YOKOZUNA-1, are reported. In RvSOD15, one of the histidine ligands of the catalytic copper center is replaced by a valine (Val87). The crystal structures of the wild type and the V87H mutant show that even though a histidine is placed at position 87, a nearby flexible loop can destabilize the coordination of His87 to the Cu atom. Model structures of other RvSODs were investigated and it was found that some of them are also unusual SODs, with features such as deletion of the electrostatic loop or β3 sheet and unusual metal-binding residues. These studies show that RvSOD15 and some other RvSODs may have evolved to lose the SOD function, suggesting that gene duplications of antioxidant proteins do not solely explain the high stress tolerance of anhydrobiotic tardigrades.

  • Organizational Affiliation

    Graduate School of Pharmaceutical Science, Osaka University, Suita City, Osaka 565-0871, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]194Ramazzottius varieornatusMutation(s): 0 
Gene Names: RvY_13070-1
Find proteins for A0A1D1VU85 (Ramazzottius varieornatus)
Explore A0A1D1VU85 
Go to UniProtKB:  A0A1D1VU85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D1VU85
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
H [auth A]
K [auth C]
M [auth D]
P [auth E]
R [auth B]
H [auth A],
K [auth C],
M [auth D],
P [auth E],
R [auth B],
T [auth F]
CU (Subject of Investigation/LOI)
Query on CU

Download Ideal Coordinates CCD File 
G [auth A]
J [auth C]
L [auth D]
O [auth E]
Q [auth B]
G [auth A],
J [auth C],
L [auth D],
O [auth E],
Q [auth B],
S [auth F]
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
I [auth A],
N [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.102α = 94.895
b = 68.049β = 108.385
c = 68.135γ = 114.4
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17K17862
Japan Society for the Promotion of Science (JSPS)Japan20K15971

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release