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PDBsum entry 1rwy

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protein ligands metals Protein-protein interface(s) links
Calcium-binding protein PDB id
1rwy
Jmol
Contents
Protein chains
109 a.a. *
Ligands
SO4 ×4
ACY
NH4
PG4
Metals
_CA ×6
Waters ×373
* Residue conservation analysis
PDB id:
1rwy
Name: Calcium-binding protein
Title: Crystal structure of rat alpha-parvalbumin at 1.05 resolution
Structure: Parvalbumin alpha. Chain: a, b, c. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Tissue: fast-twitch muscle. Gene: pvalb, pva. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.05Å     R-factor:   0.133     R-free:   0.162
Authors: C.A.Bottoms,J.P.Schuermann,S.Agah,M.T.Henzl,J.J.Tanner
Key ref:
C.A.Bottoms et al. (2004). Crystal structure of rat alpha-parvalbumin at 1.05 Angstrom resolution. Protein Sci, 13, 1724-1734. PubMed id: 15169955 DOI: 10.1110/ps.03571004
Date:
17-Dec-03     Release date:   11-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P02625  (PRVA_RAT) -  Parvalbumin alpha
Seq:
Struc:
110 a.a.
109 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   7 terms 
  Biological process     cytosolic calcium ion homeostasis   1 term 
  Biochemical function     protein homodimerization activity     4 terms  

 

 
DOI no: 10.1110/ps.03571004 Protein Sci 13:1724-1734 (2004)
PubMed id: 15169955  
 
 
Crystal structure of rat alpha-parvalbumin at 1.05 Angstrom resolution.
C.A.Bottoms, J.P.Schuermann, S.Agah, M.T.Henzl, J.J.Tanner.
 
  ABSTRACT  
 
The crystal structure of rat alpha-parvalbumin has been determined at 1.05 Angstrom resolution, using synchrotron data collected at Advanced Photon Source beamline 19-ID. After refinement with SHELX, employing anisotropic displacement parameters and riding hydrogen atoms, R = 0.132 and R(free) = 0.162. The average coordinate estimated standard deviations are 0.021 Angstrom and 0.038 Angstrom for backbone atoms and side-chain atoms, respectively. Besides providing a more precise view of the alpha-isoform than previously available, these data permit comparison with the 0.91 Angstrom structure determined for pike beta-parvalbumin. Visualization of the anisotropic displacement parameters as thermal ellipsoids yields insight into the atomic motion within the Ca(2+)-binding sites. The asymmetric unit includes three parvalbumin (PV) molecules. Interestingly, the EF site in one displays uncharacteristic flexibility. The ellipsoids for Asp-92 are particularly large and non-spherical, and the shape of the Ca(2+) ellipsoid implies significant vibrational motion perpendicular to the plane defined by the four y and z ligands. The relative dearth of crystal-packing interactions in this site suggests that the heightened flexibility may be the result of diminished intermolecular contacts. The implication is that, by impeding conformational mobility, crystal-packing forces may cause serious overestimation of EF-hand rigidity. The high quality of the data permitted 11 residues to be modeled in alternative side-chain conformations, including the two core residues, Ile-97 and Leu-105. The discrete disorder observed for Ile-97 may have functional ramifications, providing a mechanism for communicating binding status between the CD and EF binding loops and between the PV metal ion-binding domain and the N-terminal AB region.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Ribbon drawing of one of the three protein molecules in the asymmetric unit. The bound Ca ions are indicated by spheres. Figures 1, 3 Go-, and 5 Go-were created using PyMol (DeLano 2002).
Figure 5.
Figure 5. Stereoscopic view of core residues having dual side-chain conformations. (A) Ile-A97. (B) Leu-A105. The 2Fo-Fc map is contoured at 1 in each figure.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2004, 13, 1724-1734) copyright 2004.  
  Figures were selected by the author.  

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
19622856 F.Hoh, A.Cavé, M.P.Strub, J.L.Banères, and A.Padilla (2009).
Removing the invariant salt bridge of parvalbumin increases flexibility in the AB-loop structure.
  Acta Crystallogr D Biol Crystallogr, 65, 733-743.
PDB code: 3f45
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
17094115 S.J.Lee, C.C.Ju, S.L.Chu, M.S.Chien, T.H.Chan, and W.L.Liao (2007).
Molecular cloning, expression and phylogenetic analyses of parvalbumin in tilapia, Oreochromis mossambicus.
  J Exp Zool Part A Ecol Genet Physiol, 307, 51-61.  
16700049 C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.
  Proteins, 64, 404-421.  
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