2OTE | pdb_00002ote

Crystal structure of a monomeric cyan fluorescent protein in the photobleached state

• PDB DOI: https://doi.org/10.2210/pdb2OTE/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Clavularia sp.
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-02-07 Released: 2007-04-03 
• Deposition Author(s): Henderson, J.N., Ai, H., Campbell, R.E., Remington, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.261 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structural basis for reversible photobleaching of a green fluorescent protein homologue.

Henderson, J.N., Ai, H.W., Campbell, R.E., Remington, S.J.

(2007) Proc Natl Acad Sci U S A 104: 6672-6677

• PubMed: 17420458 
• DOI: https://doi.org/10.1073/pnas.0700059104
• Primary Citation Related Structures: 
  2OTB, 2OTE


• PubMed Abstract: 
  

  Fluorescent protein (FP) variants that can be reversibly converted between fluorescent and nonfluorescent states have proven to be a catalyst for innovation in the field of fluorescence microscopy. However, the structural basis of the process remains poorly understood. High-resolution structures of a FP derived from Clavularia in both the fluorescent and the light-induced nonfluorescent states reveal that the rapid and complete loss of fluorescence observed upon illumination with 450-nm light results from cis-trans isomerization of the chromophore. The photoinduced change in configuration from the well ordered cis isomer to the highly nonplanar and disordered trans isomer is accompanied by a dramatic rearrangement of internal side chains. Taken together, the structures provide an explanation for the loss of fluorescence upon illumination, the slow light-independent recovery, and the rapid light-induced recovery of fluorescence. The fundamental mechanism appears to be common to all of the photoactivatable and reversibly photoswitchable FPs reported to date.

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Organizational Affiliation: 
• Departments of Chemistry and Physics, and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.66 kDa 
• Atom Count: 4,007 
• Modeled Residue Count: 428 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GFP-like fluorescent chromoprotein cFP484	A, B	214	Clavularia sp.	Mutation(s): 21  Gene Names: cFP484
UniProt
Find proteins for Q9U6Y3 (Clavularia sp.) Explore Q9U6Y3  Go to UniProtKB:  Q9U6Y3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PIA	A, B	L-PEPTIDE LINKING	C14 H15 N3 O4		ALA, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.261 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.489	α = 90
b = 66.31	β = 90
c = 97.203	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
SHELX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
SHELXL	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-03 
Deposition Author(s): Henderson, J.N., Ai, H., Campbell, R.E., Remington, S.J.

Revision History  

• Version 1.0: 2007-04-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-02-22
  Changes: Other
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.6: 2023-11-15
  Changes: Data collection
• Version 2.0: 2026-03-18
  Changes: Polymer sequence, Structure summary