Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 24.34 kDa 
• Atom Count: 1677 
• Residue Count: 170 
• Unique protein chains: 1

7DF2

Crystal structure of a C2 domain protein from Ramazzottius varieornatus

• DOI: 10.2210/pdb7DF2/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Ramazzottius varieornatus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-11-06 Released: 2020-12-09 
• Deposition Author(s): Fukuda, Y., Inoue, T.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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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 

Literature

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

Fukuda, Y., Inoue, T.

(2020) Protein Sci 

• PubMed: 33226149 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C2 domain protein	A	212	Ramazzottius varieornatus	Mutation(s): 0  Gene Names: RvY_00338-1, RvY_00338.1, RvY_00338
Find proteins for A0A1D1UCW7 (Ramazzottius varieornatus) Explore A0A1D1UCW7  Go to UniProtKB:  A0A1D1UCW7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-glucopyranose-(1-1)-alpha-D-glucopyranose	C	2		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.212 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: P 4₁ 2₁ 2
• Diffraction Data DOI: 10.18430/m37df2 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.916	α = 90
b = 62.916	β = 90
c = 100.499	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJAX191C
Japan Society for the Promotion of Science (JSPS)	Japan	20K15971

Revision History 

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