2R2I | pdb_00002r2i

Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.251 (Depositor) 
  • R-Value Work: 
    0.218 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2R2I

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Stabilizing function for myristoyl group revealed by the crystal structure of a neuronal calcium sensor, guanylate cyclase-activating protein 1.

Stephen, R.Bereta, G.Golczak, M.Palczewski, K.Sousa, M.C.

(2007) Structure 15: 1392-1402

  • DOI: https://doi.org/10.1016/j.str.2007.09.013
  • Primary Citation Related Structures: 
    2R2I

  • PubMed Abstract: 

    Guanylate cyclase-activating proteins (GCAPs) are Ca(2+)-binding proteins myristoylated at the N terminus that regulate guanylate cyclases in photoreceptor cells and belong to the family of neuronal calcium sensors (NCS). Many NCS proteins display a recoverin-like "calcium-myristoyl switch" whereby the myristoyl group, buried inside the protein in the Ca(2+)-free state, becomes fully exposed upon Ca(2+) binding. Here we present a 2.0 A resolution crystal structure of myristoylated GCAP1 with Ca(2+) bound. The acyl group is buried inside Ca(2+)-bound GCAP1. This is in sharp contrast to Ca(2+)-bound recoverin, where the myristoyl group is solvent exposed. Furthermore, we provide direct evidence that the acyl group in GCAP1 remains buried in the Ca(2+)-free state and does not undergo switching. A pronounced kink in the C-terminal helix and the presence of the myristoyl group allow clustering of sequence elements crucial for GCAP1 activity.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA.

Macromolecule Content 

  • Total Structure Weight: 23.39 kDa 
  • Atom Count: 1,598 
  • Modeled Residue Count: 184 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanylyl cyclase-activating protein 1198Gallus gallusMutation(s): 1 
Gene Names: GUCA1AGCAP1
UniProt
Find proteins for P79880 (Gallus gallus)
Explore P79880 
Go to UniProtKB:  P79880
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP79880
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MYR

Query on MYR



Download:Ideal Coordinates CCD File
E [auth A]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
BME

Query on BME



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
I [auth A]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.251 (Depositor) 
  • R-Value Work:  0.218 (Depositor), 0.232 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.333α = 90
b = 73.333β = 90
c = 73.229γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2007-12-11 
  • Deposition Author(s): Stephen, R.

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations