2Y4Q

Solution structure of the EF-hand domain of Human Polycystin 2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 25 
  • Conformers Submitted: 20 
  • Selection Criteria: NO VIOLATIONS > 0.25A 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

A High-Resolution Structure of the EF-Hand Domain of Human Polycystin-2.

Allen, M.D.Qamar, S.Vadivelu, M.K.Sandford, R.N.Bycroft, M.

(2014) Protein Sci 23: 1301

  • DOI: https://doi.org/10.1002/pro.2513
  • Primary Citation of Related Structures:  
    2Y4Q

  • PubMed Abstract: 

    Autosomal dominant polycystic kidney disease (ADPKD) affects over 1:1000 of the worldwide population and is caused by mutations in two genes, PKD1 and PKD2. PKD2 encodes a 968-amino acid membrane spanning protein, Polycystin-2 (PC-2), which is a member of the TRP ion channel family. The C-terminal cytoplasmic tail contains an EF-hand motif followed by a short coiled-coil domain. We have determined the structure of the EF-hand region of PC-2 using NMR spectroscopy. The use of different boundaries, compared with those used in previous studies, have enabled us to determine a high resolution structure and show that the EF hand motif forms a standard calcium-binding pocket. The affinity of this pocket for calcium has been measured and mutants that both decrease and increase its affinity for the metal ion have been created.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POLYCYSTIN-279Homo sapiensMutation(s): 0 
Gene Names: PKD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13563 (Homo sapiens)
Explore Q13563 
Go to UniProtKB:  Q13563
PHAROS:  Q13563
GTEx:  ENSG00000118762 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13563
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 25 
  • Conformers Submitted: 20 
  • Selection Criteria: NO VIOLATIONS > 0.25A 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2014-07-16
    Changes: Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.2: 2014-08-27
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Data collection, Source and taxonomy
  • Version 2.0: 2024-05-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other