3EVP | pdb_00003evp

crystal structure of circular-permutated EGFP

• PDB DOI: https://doi.org/10.2210/pdb3EVP/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-10-13 Released: 2008-12-09 
• Deposition Author(s): Wang, Q., Shui, B., Kotlikoff, M.I., Sondermann, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.174 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.128 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Literature

Structural Basis for Calcium Sensing by GCaMP2.

Wang, Q., Shui, B., Kotlikoff, M.I., Sondermann, H.

(2008) Structure 16: 1817-1827

• PubMed: 19081058 
• DOI: https://doi.org/10.1016/j.str.2008.10.008
• Primary Citation Related Structures: 
  3EVP, 3EVR, 3EVU, 3EVV


• PubMed Abstract: 
  

  Genetically encoded Ca(2+) indicators are important tools that enable the measurement of Ca(2+) dynamics in a physiologically relevant context. GCaMP2, one of the most robust indicators, is a circularly permutated EGFP (cpEGFP)/M13/calmodulin (CaM) fusion protein that has been successfully used for studying Ca(2+) fluxes in vivo in the heart and vasculature of transgenic mice. Here we describe crystal structures of bright and dim states of GCaMP2 that reveal a sophisticated molecular mechanism for Ca(2+) sensing. In the bright state, CaM stabilizes the fluorophore in an ionized state similar to that observed in EGFP. Mutational analysis confirmed critical interactions between the fluorophore and elements of the fused peptides. Solution scattering studies indicate that the Ca(2+)-free form of GCaMP2 is a compact, predocked state, suggesting a molecular basis for the relatively rapid signaling kinetics reported for this indicator. These studies provide a structural basis for the rational design of improved Ca(2+)-sensitive probes.

---

Organizational Affiliation: 
• Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.

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: 27.35 kDa 
• Atom Count: 2,231 
• Modeled Residue Count: 224 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,Green fluorescent protein	A	243	Aequorea victoria	Mutation(s): 1  Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212  Go to UniProtKB:  P42212

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO	A	L-PEPTIDE LINKING	C15 H17 N3 O5		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.174 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.128 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.06	α = 90
b = 62.22	β = 90
c = 69.45	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Wang, Q., Shui, B., Kotlikoff, M.I., Sondermann, H.

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-07-19
  Changes: Advisory, Database references, Source and taxonomy, Structure summary
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-09
  Changes: Structure summary
• Version 2.0: 2026-03-18
  Changes: Polymer sequence