Crystal structure of a C2 domain protein from Ramazzottius varieornatus

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

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Structural insights into a C2 domain protein specifically found in tardigrades.

Fukuda, Y.Inoue, T.

(2021) Protein Sci 30: 513-518

  • DOI: https://doi.org/10.1002/pro.4002
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Some tardigrades can survive extremely desiccated conditions through transition into a state called anhydrobiosis. Anhydrobiotic tardigrades have proteins unique to them and they are thought to be keys to the understanding of unusual desiccation resistance. In fact, previous transcriptome data show that several tardigrade-specific proteins are significantly upregulated under desiccated conditions. However, their physiological roles and chemical properties have been ambiguous because they show low or no similarity of amino acid sequences to proteins found in other organisms. Here, we report a crystal structure of one of such proteins. This protein shows a β-sandwich structure composed of 8 β-strands, three Ca 2+ -binding sites, and hydrophobic residues on Ca 2+ -binding (CBD) loops, which resemble characteristics of C2 domain proteins. We therefore conveniently describe this protein as tardigrade C2 domain protein (TC2P). Because the C2 domain functions as a Ca 2+ -mediated membrane docking module, which is related to signal transduction or membrane trafficking, TC2Ps may play a role in Ca 2+ -triggered phenomenon under desiccated situations. Our finding provides not only structural insights into a newly discovered desiccation-related protein family but also insights into the evolution and diversity of C2 domain proteins.

  • Organizational Affiliation

    Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C2 domain protein212Ramazzottius varieornatusMutation(s): 0 
Gene Names: RvY_00338-1RvY_00338.1RvY_00338
Find proteins for A0A1D1UCW7 (Ramazzottius varieornatus)
Explore A0A1D1UCW7 
Go to UniProtKB:  A0A1D1UCW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D1UCW7
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-1)-alpha-D-glucopyranoseB [auth C]2N/A
Glycosylation Resources
GlyTouCan:  G21133VQ
GlyCosmos:  G21133VQ
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.916α = 90
b = 62.916β = 90
c = 100.499γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJAX191C
Japan Society for the Promotion of Science (JSPS)Japan20K15971

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references