PDBsum entry 1rro

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Calcium-binding protein PDB id
Protein chain
108 a.a. *
_CA ×4
Waters ×103
* Residue conservation analysis
PDB id:
Name: Calcium-binding protein
Title: Refinement of recombinant oncomodulin at 1.30 angstroms resolution
Structure: Rat oncomodulin. Chain: a. Engineered: yes
Source: Rattus rattus. Black rat. Organism_taxid: 10117. Organ: liver
1.30Å     R-factor:   0.176    
Authors: F.R.Ahmed,D.R.Rose,S.V.Evans,M.E.Pippy,R.To
Key ref: F.R.Ahmed et al. (1993). Refinement of recombinant oncomodulin at 1.30 A resolution. J Mol Biol, 230, 1216-1224. PubMed id: 8487302
27-Aug-92     Release date:   31-Oct-93    
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Protein chain
Pfam   ArchSchema ?
P02631  (ONCO_RAT) -  Oncomodulin
109 a.a.
108 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   3 terms 
  Biological process     cytosolic calcium ion homeostasis   1 term 
  Biochemical function     protein homodimerization activity     4 terms  


J Mol Biol 230:1216-1224 (1993)
PubMed id: 8487302  
Refinement of recombinant oncomodulin at 1.30 A resolution.
F.R.Ahmed, D.R.Rose, S.V.Evans, M.E.Pippy, R.To.
A refinement of the oncomodulin crystal structure at 1.30 A resolution has been carried out with X-ray data from the recombinant protein. The crystallographic R-factor values are 0.169 for 19,995 reflections in the range 6.0 to 1.30 A, which were used for the restrained least-squares refinement, and 0.176 for 20,186 observed reflections in the range 10.0 to 1.30 A. This high resolution refinement has enabled us to make more definitive statements about the molecular structure than was possible heretofore. The present model includes residues 1 to 108, the two Ca2+ of the CD and EF loops, two intermolecular Ca2+, and 103 water molecules per oncomodulin molecule. The electron density maps indicate disordered orientations for ten residues on the hydrophilic surface of the molecule. The pattern of molecular aggregation via intermolecular Ca2+, which occurs in the native rat oncomodulin structure, is also present in the recombinant oncomodulin structure. The Cys18 side-chain is not in a position that would be easily accessible for molecular dimerization via a disulphide bond. The substitution of Glu59, which is preserved in all the determined species of parvalbumin, by Asp59 in oncomodulin seems to break a stabilizing hydrogen bond in the CD loop and render the main-chain in positions 59 to 60 somewhat unstable. This instability in the CD loop, and the strong tendency of oncomodulin for molecular aggregation via intermolecular Ca2+, appear to be the two outstanding features that may account for oncomodulin's biological peculiarities.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287610 M.T.Henzl, J.J.Tanner, and A.Tan (2011).
Solution structures of chicken parvalbumin 3 in the Ca(2+) -free and Ca(2+) -bound states.
  Proteins, 79, 752-764.
PDB codes: 2kyc 2kyf
20156445 J.P.Schuermann, A.Tan, J.J.Tanner, and M.T.Henzl (2010).
Structure of avian thymic hormone, a high-affinity avian beta-parvalbumin, in the Ca2+-free and Ca2+-bound states.
  J Mol Biol, 397, 991.
PDB codes: 2kqy 3fs7
19651438 S.E.Permyakov, A.G.Bakunts, M.E.Permyakova, A.I.Denesyuk, V.N.Uversky, and E.A.Permyakov (2009).
Metal-controlled interdomain cooperativity in parvalbumins.
  Cell Calcium, 46, 163-175.  
18218708 M.T.Henzl, and J.J.Tanner (2008).
Solution structure of Ca2+-free rat alpha-parvalbumin.
  Protein Sci, 17, 431-438.
PDB code: 2jww
17766386 M.T.Henzl, and J.J.Tanner (2007).
Solution structure of Ca2+-free rat beta-parvalbumin (oncomodulin).
  Protein Sci, 16, 1914-1926.
PDB code: 2nln
16700049 C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.
  Proteins, 64, 404-421.  
16283654 M.T.Henzl, and S.Agah (2006).
Divalent ion-binding properties of the two avian beta-parvalbumins.
  Proteins, 62, 270-278.  
16227209 J.E.Debreczeni, L.Farkas, V.Harmat, C.Hetényi, I.Hajdú, P.Závodszky, K.Kohama, and L.Nyitray (2005).
Structural evidence for non-canonical binding of Ca2+ to a canonical EF-hand of a conventional myosin.
  J Biol Chem, 280, 41458-41464.
PDB code: 2bl0
14997562 A.Bhaduri, R.Ravishankar, and R.Sowdhamini (2004).
Conserved spatially interacting motifs of protein superfamilies: application to fold recognition and function annotation of genome data.
  Proteins, 54, 657-670.  
15169955 C.A.Bottoms, J.P.Schuermann, S.Agah, M.T.Henzl, and J.J.Tanner (2004).
Crystal structure of rat alpha-parvalbumin at 1.05 Angstrom resolution.
  Protein Sci, 13, 1724-1734.
PDB code: 1rwy
11742132 M.T.Henzl, W.G.Wycoff, J.D.Larson, and J.J.Likos (2002).
15N nuclear magnetic resonance relaxation studies on rat beta-parvalbumin and the pentacarboxylate variants, S55D and G98D.
  Protein Sci, 11, 158-173.  
11939594 O.V.Tsodikov, M.T.Record, and Y.V.Sergeev (2002).
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature.
  J Comput Chem, 23, 600-609.  
  10739260 I.Tsigelny, I.N.Shindyalov, P.E.Bourne, T.C.Südhof, and P.Taylor (2000).
Common EF-hand motifs in cholinesterases and neuroligins suggest a role for Ca2+ binding in cell surface associations.
  Protein Sci, 9, 180-185.  
10801337 M.T.Henzl, J.D.Larson, and S.Agah (2000).
Influence of monovalent cations on rat alpha- and beta-parvalbumin stabilities.
  Biochemistry, 39, 5859-5867.  
9636056 M.T.Henzl, R.C.Hapak, and J.J.Likos (1998).
Interconversion of the ligand arrays in the CD and EF sites of oncomodulin. Influence on Ca2+-binding affinity.
  Biochemistry, 37, 9101-9111.  
8639547 M.T.Henzl, R.C.Hapak, and E.A.Goodpasture (1996).
Introduction of a fifth carboxylate ligand heightens the affinity of the oncomodulin CD and EF sites for Ca2+.
  Biochemistry, 35, 5856-5869.  
8973640 T.L.Pauls, I.Durussel, I.D.Clark, A.G.Szabo, M.W.Berchtold, and J.A.Cox (1996).
Site-specific replacement of amino acid residues in the CD site of rat parvalbumin changes the metal specificity of this Ca2+/Mg(2+)-mixed site toward a Ca(2+)-specific site.
  Eur J Biochem, 242, 249-255.  
7896823 A.C.da Silva, J.Kendrick-Jones, and F.C.Reinach (1995).
Determinants of ion specificity on EF-hands sites. Conversion of the Ca2+/Mg2+ site of smooth muscle myosin regulatory light chain into a Ca(2+)-specific site.
  J Biol Chem, 270, 6773-6778.  
7899550 J.J.Falke, S.K.Drake, A.L.Hazard, and O.B.Peersen (1994).
Molecular tuning of ion binding to calcium signaling proteins.
  Q Rev Biophys, 27, 219-290.  
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.