1SL8

Calcium-loaded apo-aequorin from Aequorea victoria


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

All three Ca2+-binding loops of photoproteins bind calcium ions: The crystal structures of calcium-loaded apo-aequorin and apo-obelin.

Deng, L.Vysotski, E.S.Markova, S.V.Liu, Z.J.Lee, J.Rose, J.Wang, B.C.

(2005) Protein Sci 14: 663-675

  • DOI: 10.1110/ps.041142905
  • Primary Citation of Related Structures:  
    1SL7, 1SL8

  • PubMed Abstract: 
  • The crystal structures of calcium-loaded apo-aequorin and apo-obelin have been determined at resolutions 1.7A and 2.2 A, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration ...

    The crystal structures of calcium-loaded apo-aequorin and apo-obelin have been determined at resolutions 1.7A and 2.2 A, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-protein retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hyroperoxycoelenterazine, and also the same as the Ca2+-discharged obelin bound with product, coleneteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these photoproteins to sense Ca2+ concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed.


    Related Citations: 
    • Structure of the Ca2+-regulated photoprotein obelin at 1.7 resolution determined directly from its sulfur substructure
      Liu, Z.-J., Vysotski, E.S., Chen, C.-J., Rose, J., Lee, J., Wang, B.-C.
      (2000) Protein Sci 9: 2085
    • Preparation and preliminary study of crystals of the recombinant calcium-regulated photoprotein obelin from the bioluminescent hydroid Obelia longissima
      Vysotski, E.S., Liu, Z.-J., Rose, J., Wang, B.-C., Lee, J.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 1965
    • Structural basis for the emission of violet bioluminescence from a W92F obelin mutant
      Deng, L., Vysotski, E.S., Liu, Z.-J., Markova, S.V., Malikova, N.P., Lee, J., Rose, J., Wang, B.-C.
      (2001) FEBS Lett 506: 281
    • Violet Bioluminescence and Fast Kinetics from W92F Obelin: Structure-Based Proposals for the Bioluminescence Triggering and the Identification of the Emitting Species
      Vysotski, E.S., Liu, Z.-J., Markova, S.V., Blinks, J., Deng, L., Frank, L.A., Herko, M., Malikova, N.P., Rose, J.P., Wang, B.-C., Lee, J.
      (2003) Biochemistry 42: 6013
    • Atomic resolution structure of obelin: Soaking with calcium enhances electron density of the second oxygen atom substituted at the C2-position of coelenterazine
      Liu, Z.-J., Vysotski, E.S., Deng, L., Lee, J., Rose, J., Wang, B.-C.
      (2003) Biochem Biophys Res Commun 311: 433
    • Preparation and X-ray Crystallographic Analysis of the Ca2+-discharged Photoprotein Obelin
      Deng, L., Markova, S.V., Vysotski, E.S., Liu, Z.-J., Lee, J., Rose, J., Wang, B.-C.
      () To be published --: --

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aequorin 1A191Aequorea victoriaMutation(s): 0 
UniProt
Find proteins for P07164 (Aequorea victoria)
Explore P07164 
Go to UniProtKB:  P07164
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.371α = 90
b = 54.371β = 90
c = 135.109γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance