Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27205.22 
• Atom Count: 1817 
• Residue Count: 236 
• Unique protein chains: 1

1F09

CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP) VARIANT YFP-H148Q WITH TWO BOUND IODIDES

• DOI: 10.2210/pdb1F09/pdb

• Classification: LUMINESCENT PROTEIN
• Organism(s): Aequorea victoria
• Expression System: Escherichia coli
• Mutation(s): 5 


• Deposited: 2000-05-15 Released: 2000-11-17 
• Deposition Author(s): Wachter, R.M., Yarbrough, D., Kallio, K., Remington, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Work: 0.204 

Literature

Crystallographic and energetic analysis of binding of selected anions to the yellow variants of green fluorescent protein.

Wachter, R.M., Yarbrough, D., Kallio, K., Remington, S.J.

(2000) J.Mol.Biol. 301: 157-171

• PubMed: 10926499 
• DOI: 10.1006/jmbi.2000.3905
• Primary Citation of Related Structures:  
  1F0B


• PubMed Abstract: 
  

The fluorescence emission of yellow fluorescent proteins (YFPs) has been shown to respond rapidly and reversibly to changes in the concentration of some small anions such as halides; this allows for the use of YFPs as genetically encodable Cl(-) sensors that may be targeted to specific organelles in living cells. Fluorescence is suppressed due to protonation of the chromophore upon anion binding, with a stronger level of interaction at low pH values. At pH 6.0, the apparent dissociation constant (K(app)) for Cl(-) is 32 mM for YFP and 22 mM for YFP-H148Q, whereas at pH 7.5, K(app) is 777 mM and 154 mM, respectively. In the cytosol, YFP-H148Q appears most promising as a halide sensor due to its high degree of sensitivity towards I(-) (K(app)=23 mM at pH 7.5). To aid in the design of variants with improved levels of specificity and affinity for Cl(-), we solved apo and I(-)-bound crystal structures of YFP-H148Q to 2.1 A resolution. The halide-binding site is found near van der Waals contact with the chromophore imidazolinone oxygen atom, in a small buried cavity adjacent to Arg96, which provides electrostatic stabilization. The halide ion is hydrogen bonded to the phenol group of T203Y, consistent with a mutational analysis that indicates that T203Y is indispensible for tight binding. A series of conformational changes occurs in the amphiphilic site upon anion binding, which appear to be propagated to the beta-bulge region around residue 148 on the protein surface. Anion binding raises the chromophore pK(a) values, since delocalization of the phenolate negative charge over the chromophore skeleton is suppressed. Extraction of microscopic binding constants for the linked equilibrium between anion and proton binding indicates that anion selectivity by YFP is related to hydration forces. Specific suggestions to improve Cl(-) binding to YFP-H148Q based on size and hydration energy are proposed.

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Related Citations: 

• Sensitivity of the Yellow Variant of Green Fluorescent Protein to Halides and Nitrate
  Wachter, R.M.,Remington, S.J.
  (1999) CURR.BIOL. 9: R628




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Organizational Affiliation: 

Institute of Molecular Biology Departments of Physics and Biology, University of Oregon, Eugene, OR, 97403, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
GREEN FLUORESCENT PROTEIN	A	238	Aequorea victoria	Mutation(s): 5  Gene Names: GFP
Find proteins for P42212 (Aequorea victoria) Go to UniProtKB:  P42212

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
IOD	A	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CR2	A	L-PEPTIDE LINKING	C13 H13 N3 O4		GLY, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Work: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 51.197	α = 90.00
b = 62.818	β = 90.00
c = 68.667	γ = 90.00

Software Package:

Software Name	Purpose
TNT	refinement
DENZO	data reduction
TNT	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-05-15 
• Released Date: 2000-11-17 
• Deposition Author(s): Wachter, R.M., Yarbrough, D., Kallio, K., Remington, S.J.

Revision History 

• Version 1.0: 2000-11-17
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance