2WUR

Atomic resolution structure of GFP measured on a rotating anode


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.9 Å
  • R-Value Free: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Visualizing Proton Antenna in a High-Resolution Green Fluorescent Protein Structure.

Shinobu, A.Palm, G.J.Schierbeek, A.J.Agmon, N.

(2010) J.Am.Chem.Soc. 132: 11093

  • DOI: 10.1021/ja1010652

  • PubMed Abstract: 
  • "Proton-collecting antenna" are conjectured to consist of several carboxylates within hydrogen-bond (HB) networks on the surface of proteins, which funnel protons to the orifice of an internal proton wire leading to the protein's active site. Yet suc ...

    "Proton-collecting antenna" are conjectured to consist of several carboxylates within hydrogen-bond (HB) networks on the surface of proteins, which funnel protons to the orifice of an internal proton wire leading to the protein's active site. Yet such constructions were never directly visualized. Here we report an X-ray structure of green fluorescent protein (GFP) of the highest resolution to date (0.9 A). It allows the identification of some pivotal hydrogen atoms pertinent to uncertainties concerning the protonation state of the chromophore. Applying a computer algorithm for mapping proton wires in proteins reveals the previously observed "active site wire" connecting Glu222 with the surface carboxylate Glu5. In addition, it is now possible to identify what appears to be a proton-collecting apparatus of GFP. It consists of a negative surface patch containing carboxylates, threonines, and water molecules, connected by a HB network to Glu5. Furthermore, we detect exit points via Asn146 and His148 to a hydrophobic surface region. The more extensive HB network of the present structure, as compared with earlier GFP structures, is not accidental. A systematic investigation of over 100 mutants shows a clear correlation between the observed water content of GFP X-ray structures and their resolution. With increasing water content, the proton wires become progressively larger. These findings corroborate the scenario in which the photodissociated proton from wild-type GFP can leak outside, whereafter another proton is recruited via the proton-collecting apparatus reported herein.


    Related Citations: 
    • The Structural Basis for Spectral Variations in Green Fluorescent Protein.
      Palm, G.J.,Zdanov, A.,Gaitanaris, G.A.,Stauber, R.,Pavlakis, G.N.,Wlodawer, A.
      (1997) Nat.Struct.Mol.Biol. 4: 361


    Organizational Affiliation

    The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GREEN FLUORESCENT PROTEIN
A
238Aequorea victoriaMutation(s): 4 
Gene Names: GFP
Find proteins for P42212 (Aequorea victoria)
Go to UniProtKB:  P42212
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPA
Query on IPA

Download SDF File 
Download CCD File 
A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

Download SDF File 
Download CCD File 
A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GYS
Query on GYS
A
L-PEPTIDE LINKINGC14 H15 N3 O5SER, TYR, GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.9 Å
  • R-Value Free: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.987α = 90.00
b = 59.050β = 90.00
c = 67.700γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
SADABSdata scaling
SAINTdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2014-03-05
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2017-07-05
    Type: Data collection
  • Version 1.3: 2019-05-08
    Type: Data collection, Derived calculations, Experimental preparation
  • Version 1.4: 2019-10-23
    Type: Data collection, Database references, Other