7DF2

Crystal structure of a C2 domain protein from Ramazzottius varieornatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report



Literature

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

Fukuda, Y.Inoue, T.

(2020) Protein Sci 

  • DOI: 10.1002/pro.4002
  • Primary Citation of Related Structures:  
    7DF2

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C2 domain proteinA212Ramazzottius varieornatusMutation(s): 0 
Gene Names: RvY_00338-1RvY_00338.1RvY_00338
Find proteins for A0A1D1UCW7 (Ramazzottius varieornatus)
Explore A0A1D1UCW7 
Go to UniProtKB:  A0A1D1UCW7
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-glucopyranose-(1-1)-alpha-D-glucopyranose
C
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
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
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-11-06 
  • Released Date: 2020-12-09 
  • Deposition Author(s): Fukuda, Y., Inoue, T.

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

Revision History 

  • Version 1.0: 2020-12-09
    Type: Initial release