4YI9

Crystal structure of non-myristoylated E153A recoverin at 1.35 A resolution with a sodium ion bound to EF-hand 2 and calcium ion bound to EF-hand 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Recoverin with Calcium Ions Bound to Both Functional EF Hands.

Kumar, R.P.Ranaghan, M.J.Ganjei, A.Y.Oprian, D.D.

(2015) Biochemistry 54: 7222-7228

  • DOI: 10.1021/acs.biochem.5b01160
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recoverin (Rv), a small Ca(2+)-binding protein that inhibits rhodopsin kinase (RK), has four EF hands, two of which are functional (EF2 and EF3). Activation requires Ca(2+) in both EF hands, but crystal structures have never been observed with Ca(2+) ...

    Recoverin (Rv), a small Ca(2+)-binding protein that inhibits rhodopsin kinase (RK), has four EF hands, two of which are functional (EF2 and EF3). Activation requires Ca(2+) in both EF hands, but crystal structures have never been observed with Ca(2+) ions in both sites; all previous structures have Ca(2+) bound to only EF3. We suspected that this was due to an intermolecular crystal contact between T80 and a surface glutamate (E153) that precluded coordination of a Ca(2+) ion in EF2. We constructed the E153A mutant, determined its X-ray crystal structure to 1.2 Å resolution, and showed that two Ca(2+) ions are bound, one in EF3 and one in EF2. Additionally, several other residues are shown to adopt conformations in the 2Ca(2+) structure not seen previously and not seen in a second structure of the E153A mutant containing Na(+) instead of Ca(2+) in the EF2 site. The side-chain rearrangements in these residues form a 28 Å allosteric cascade along the surface of the protein connecting the Ca(2+)-binding site of EF2 with the active-site pocket responsible for binding RK.


    Organizational Affiliation

    Department of Biochemistry, Brandeis University , Waltham, Massachusetts 02454, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Recoverin
A
201Bos taurusMutation(s): 1 
Gene Names: RCVRN (RCV1)
Find proteins for P21457 (Bos taurus)
Go to Gene View: RCVRN
Go to UniProtKB:  P21457
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.152 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 85.340α = 90.00
b = 85.340β = 90.00
c = 58.750γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States--

Revision History 

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2015-12-30
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations