3CF6

Structure of Epac2 in complex with cyclic-AMP and Rap

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B

Rehmann, H., Arias-Palomo, E., Hadders, M.A., Schwede, F., Llorca, O., Bos, J.L.

(2008) Nature 455: 124-127

  • DOI: 10.1038/nature07187
  • Primary Citation of Related Structures:  
    3CF6

  • PubMed Abstract: 

    • Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell adhesion and insulin secretion. Here we have determined the ...

    Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell adhesion and insulin secretion. Here we have determined the structure of Epac2 in complex with a cAMP analogue (Sp-cAMPS) and RAP1B by X-ray crystallography and single particle electron microscopy. The structure represents the cAMP activated state of the Epac2 protein with the RAP1B protein trapped in the course of the exchange reaction. Comparison with the inactive conformation reveals that cAMP binding causes conformational changes that allow the cyclic nucleotide binding domain to swing from a position blocking the Rap binding site towards a docking site at the Ras exchange motif domain.

    Related Citations: 
    • Structure of the cyclic-AMP-responsive exchange factor Epac2 in its auto-inhibited state
      Rehmann, H., Das, J., Knipscheer, P., Wittinghofer, A., Bos, J.L.
      (2006) Nature 439: 625
    • Structure and regulation of the cAMP-binding domains of Epac2
      Rehmann, H., Prakash, B., Wolf, E., Rueppel, A., de Rooij, J., Bos, J.L., Wittinghofer, A.
      (2003) Nat Struct Biol 10: 26
    Organizational Affiliation: 

    Department of Physiological Chemistry, Centre for Biomedical Genetics and Cancer Genomics Centre, University Medical Center, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands. h.rehmann@UMCutrecht.nl



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rap guanine nucleotide exchange factor (GEF) 4 E694Mus musculusMutation(s): 0 
Gene Names: Rapgef4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rap-1b R167Homo sapiensMutation(s): 0 
Gene Names: RAP1B, OK/SW-cl.11
EC: 3.6.5.2
Find proteins for P61224 (Homo sapiens)
Explore P61224 
Go to UniProtKB:  P61224
NIH Common Fund Data Resources
PHAROS:  P61224
GTEx:  ENSG00000127314
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SP1
Query on SP1
Download Ideal Coordinates CCD File 
E
6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL
C10 H12 N5 O5 P S
SMPNJFHAPJOHPP-LHKKBNDGSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.367α = 90
b = 149.025β = 90
c = 225.291γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-05
    Changes: Derived calculations