4F7Z

Conformational dynamics of exchange protein directly activated by cAMP

• PDB DOI:  https://doi.org/10.2210/pdb4F7Z/pdb

• Classification: EXOCYTOSIS
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-05-16 Released: 2012-10-03 
• Deposition Author(s): White, M.A., Tsalkova, T.N., Mei, F.C., Liu, T., Woods, V.L., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.282 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Literature

Structural analyses of a constitutively active mutant of exchange protein directly activated by cAMP.

White, M.A., Li, S., Tsalkova, T., Mei, F.C., Liu, T., Woods, V.L., Cheng, X.

(2012) PLoS One 7: e49932-e49932

• PubMed: 23189173 
• DOI: https://doi.org/10.1371/journal.pone.0049932
• Primary Citation of Related Structures:  
  4F7Z


• PubMed Abstract: 
  

Exchange proteins directly activated by cAMP (EPACs) are important allosteric regulators of cAMP-mediated signal transduction pathways. To understand the molecular mechanism of EPAC activation, we have combined site-directed mutagenesis, X-ray crystallography, and peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS) to probe the structural and conformational dynamics of EPAC2-F435G, a constitutively active EPAC2 mutant. Our study demonstrates that conformational dynamics plays a critical role in cAMP-induced EPAC activation. A glycine mutation at 435 position shifts the equilibrium of conformational dynamics towards the extended active conformation.

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Organizational Affiliation: 

Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, United States of America.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.71 kDa 
• Atom Count: 7,666 
• Modelled Residue Count: 946 
• Deposited Residue Count: 999 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rap guanine nucleotide exchange factor 4	A	999	Mus musculus	Mutation(s): 1  Gene Names: Rapgef4, Cgef2, Epac2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9EQZ6 (Mus musculus) Explore Q9EQZ6  Go to UniProtKB:  Q9EQZ6
IMPC:  MGI:1917723

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.282 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.72	α = 90
b = 95.35	β = 90
c = 181.84	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): White, M.A., Tsalkova, T.N., Mei, F.C., Liu, T., Woods, V.L., Cheng, X.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description