3KPX | pdb_00003kpx

Crystal Structure Analysis of photoprotein clytin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.219 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

NMR derived topology of a GFP-photoprotein energy transfer complex

Titushin, M.S.Feng, Y.Stepanyuk, G.A.Li, Y.Markova, S.V.Golz, S.Wang, B.-C.Lee, J.Wang, J.Vysotski, E.S.Liu, Z.-J.

(2010) J Biological Chem 285: 40891-40900

  • DOI: https://doi.org/10.1074/jbc.M110.133843
  • Primary Citation Related Structures: 
    3KPX

  • PubMed Abstract: 

    Förster resonance energy transfer within a protein-protein complex has previously been invoked to explain emission spectral modulation observed in several bioluminescence systems. Here we present a spatial structure of a complex of the Ca(2+)-regulated photoprotein clytin with its green-fluorescent protein (cgGFP) from the jellyfish Clytia gregaria, and show that it accounts for the bioluminescence properties of this system in vitro. We adopted an indirect approach of combining x-ray crystallography determined structures of the separate proteins, NMR spectroscopy, computational docking, and mutagenesis. Heteronuclear NMR spectroscopy using variously (15)N,(13)C,(2)H-enriched proteins enabled assignment of backbone resonances of more than 94% of the residues of both proteins. In a mixture of the two proteins at millimolar concentrations, complexation was inferred from perturbations of certain (1)H-(15)N HSQC-resonances, which could be mapped to those residues involved at the interaction site. A docking computation using HADDOCK was employed constrained by the sites of interaction, to deduce an overall spatial structure of the complex. Contacts within the clytin-cgGFP complex and electrostatic complementarity of interaction surfaces argued for a weak protein-protein complex. A weak affinity was also observed by isothermal titration calorimetry (K(D) = 0.9 mM). Mutation of clytin residues located at the interaction site reduced the degree of protein-protein association concomitant with a loss of effectiveness of cgGFP in color-shifting the bioluminescence. It is suggested that this clytin-cgGFP structure corresponds to the transient complex previously postulated to account for the energy transfer effect of GFP in the bioluminescence of aequorin or Renilla luciferase.


  • Organizational Affiliation
    • National Laboratory of Biomacromolecules, Institute of Biophysics Chinese Academy of Sciences, Datun Road 15, Beijing 100101, China.

Macromolecule Content 

  • Total Structure Weight: 22.95 kDa 
  • Atom Count: 1,678 
  • Modeled Residue Count: 189 
  • Deposited Residue Count: 198 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apophotoprotein clytin-3198Clytia gregariaMutation(s): 0 
EC: 1.13.12.5
UniProt
Find proteins for D7PM14 (Clytia gregaria)
Explore D7PM14 
Go to UniProtKB:  D7PM14
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7PM14
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.219 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.166 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.392α = 90
b = 68.932β = 90
c = 115.348γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Structure summary, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description