PDBsum entry 3dpz

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protein links
Luminescent protein PDB id
Jmol PyMol
Protein chain
231 a.a. *
Waters ×205
* Residue conservation analysis
PDB id:
Name: Luminescent protein
Title: Structure of the yellow fluorescent protein citrine frozen at 4000 atmospheres number 3: structure 25 in a series of 26 high pressure structures
Structure: Green fluorescent protein. Chain: a. Engineered: yes. Mutation: yes
Source: Aequorea victoria. Jellyfish. Organism_taxid: 6100. Gene: gfp. Expressed in: escherichia coli.
1.70Å     R-factor:   0.224     R-free:   0.294
Authors: B.Barstow,C.U.Kim
Key ref:
B.Barstow et al. (2008). Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift. Proc Natl Acad Sci U S A, 105, 13362-13366. PubMed id: 18768811 DOI: 10.1073/pnas.0802252105
09-Jul-08     Release date:   23-Sep-08    
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Protein chain
Pfam   ArchSchema ?
P42212  (GFP_AEQVI) -  Green fluorescent protein
238 a.a.
231 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   1 term 
  Biological process     generation of precursor metabolites and energy   3 terms 
  Biochemical function     molecular_function     1 term  


DOI no: 10.1073/pnas.0802252105 Proc Natl Acad Sci U S A 105:13362-13366 (2008)
PubMed id: 18768811  
Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift.
B.Barstow, N.Ando, C.U.Kim, S.M.Gruner.
A protein molecule is an intricate system whose function is highly sensitive to small external perturbations. However, no examples that correlate protein function with progressive subangstrom structural perturbations have thus far been presented. To elucidate this relationship, we have investigated a fluorescent protein, citrine, as a model system under high-pressure perturbation. The protein has been compressed to produce deformations of its chromophore by applying a high-pressure cryocooling technique. A closely spaced series of x-ray crystallographic structures reveals that the chromophore undergoes a progressive deformation of up to 0.8 A at an applied pressure of 500 MPa. It is experimentally demonstrated that the structural motion is directly correlated with the progressive fluorescence shift of citrine from yellow to green under these conditions. This protein is therefore highly sensitive to subangstrom deformations and its function must be understood at the subangstrom level. These results have significant implications for protein function prediction and biomolecule design and engineering, because they suggest methods to tune protein function by modification of the protein scaffold.
  Selected figure(s)  
Figure 1.
The citrine molecule and citrine's chromophore.
Figure 4.
Average center of mass positions of the main chromophore phenol and imidazolinone rings in the coordinate system defined in Fig. 3. Error bars were estimated by Cruickshank's formula. Fits are shown as solid gray lines.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22419154 Y.Kung, N.Ando, T.I.Doukov, L.C.Blasiak, G.Bender, J.Seravalli, S.W.Ragsdale, and C.L.Drennan (2012).
Visualizing molecular juggling within a B12-dependent methyltransferase complex.
  Nature, 484, 265-269.
PDB codes: 4djd 4dje 4djf
21275639 M.D.Collins, C.U.Kim, and S.M.Gruner (2011).
High-pressure protein crystallography and NMR to explore protein conformations.
  Annu Rev Biophys, 40, 81-98.  
21169696 U.Englich, I.A.Kriksunov, R.A.Cerione, M.J.Cook, R.Gillilan, S.M.Gruner, Q.Huang, C.U.Kim, W.Miller, S.Nielsen, D.Schuller, S.Smith, and D.M.Szebenyi (2011).
Microcrystallography, high-pressure cryocooling and BioSAXS at MacCHESS.
  J Synchrotron Radiat, 18, 70-73.  
20483346 E.Girard, S.Marchal, J.Perez, S.Finet, R.Kahn, R.Fourme, G.Marassio, A.C.Dhaussy, T.Prangé, M.Giffard, F.Dulin, F.Bonneté, R.Lange, J.H.Abraini, M.Mezouar, and N.Colloc'h (2010).
Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure.
  Biophys J, 98, 2365-2373.
PDB code: 3f2m
19751677 B.Barstow, N.Ando, C.U.Kim, and S.M.Gruner (2009).
Coupling of pressure-induced structural shifts to spectral changes in a yellow fluorescent protein.
  Biophys J, 97, 1719-1727.  
19258453 C.U.Kim, B.Barstow, M.W.Tate, and S.M.Gruner (2009).
Evidence for liquid water during the high-density to low-density amorphous ice transition.
  Proc Natl Acad Sci U S A, 106, 4596-4600.  
19416064 R.Fourme, E.Girard, R.Kahn, A.C.Dhaussy, and I.Ascone (2009).
Advances in high-pressure biophysics: status and prospects of macromolecular crystallography.
  Annu Rev Biophys, 38, 153-171.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.