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PDBsum entry 1rjv
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protein metals links
Metal binding protein PDB id
1rjv

 

 

 

 

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Contents
Protein chain
110 a.a. *
Metals
_CA ×2
* Residue conservation analysis
PDB id:
1rjv
Name: Metal binding protein
Title: Solution structure of human alpha-parvalbumin refined with a paramagnetism-based strategy
Structure: Parvalbumin alpha. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: pvalb. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 19 models
Authors: I.Baig,I.Bertini,C.Del Bianco,Y.K.Gupta,Y.M.Lee,C.Luchinat, A.Quattrone,Structural Proteomics In Europe (Spine)
Key ref:
I.Baig et al. (2004). Paramagnetism-based refinement strategy for the solution structure of human alpha-parvalbumin. Biochemistry, 43, 5562-5573. PubMed id: 15122922 DOI: 10.1021/bi035879k
Date:
20-Nov-03     Release date:   25-May-04    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20472  (PRVA_HUMAN) -  Parvalbumin alpha from Homo sapiens
Seq:
Struc: 		110 a.a.
110 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1021/bi035879k Biochemistry 43:5562-5573 (2004)
PubMed id: 15122922  
 
 
Paramagnetism-based refinement strategy for the solution structure of human alpha-parvalbumin.
I.Baig, I.Bertini, C.Del Bianco, Y.K.Gupta, Y.M.Lee, C.Luchinat, A.Quattrone.
 
  ABSTRACT  
 
In the frame of a research aimed at the detailed structural characterization of human calcium-binding proteins of the EF-hand family, the solution structure of human alpha-parvalbumin has been solved by NMR and refined with the help of substitution of the Ca(2+) ion in the EF site with the paramagnetic Dy(3+) ion. A simple (1)H-(15)N HSQC spectrum allowed the NH assignments based on the properties of Dy(3+). This allowed us to exploit pseudocontact shifts and residual dipolar couplings for solution structure refinement. The backbone and heavy atom RMSD are 0.55 +/- 0.08 and 1.02 +/- 0.08 A, respectively, and decrease to 0.39 +/- 0.05 and 0.90 +/- 0.06 A upon refinement with paramagnetism-based restraints. The RMSD for the metal itself in the EF site in the refined structure is 0.26 +/- 0.12 A. Backbone NH R(1), R(2), and NOE measured at two temperatures show the protein to be relatively rigid. The NH orientations are well determined by the paramagnetism-based restraints. This allows us to detect small but significant local structural differences with the orthologue protein from rat, whose X-ray structure is available at 2.0 A resolution. All differences are related to local changes in the amino acidic composition.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21241884 D.S.Wishart (2011).
Interpreting protein chemical shift data.
  Prog Nucl Magn Reson Spectrosc, 58, 62-87.  
20633251 K.Kokoszyńska, L.Rychlewski, and L.S.Wyrwicz (2010).
Distant homologs of anti-apoptotic factor HAX1 encode parvalbumin-like calcium binding proteins.
  BMC Res Notes, 3, 197.  
18237407 N.Furnham, P.I.de Bakker, S.Gore, D.F.Burke, and T.L.Blundell (2008).
Comparative modelling by restraint-based conformational sampling.
  BMC Struct Biol, 8, 7.  
17180551 C.Eichmüller, and N.R.Skrynnikov (2007).
Observation of microsecond time-scale protein dynamics in the presence of Ln3+ ions: application to the N-terminal domain of cardiac troponin C.
  J Biomol NMR, 37, 79-95.  
17910025 M.John, and G.Otting (2007).
Strategies for measurements of pseudocontact shifts in protein NMR spectroscopy.
  Chemphyschem, 8, 2309-2313.  
17096205 M.John, M.J.Headlam, N.E.Dixon, and G.Otting (2007).
Assignment of paramagnetic (15)N-HSQC spectra by heteronuclear exchange spectroscopy.
  J Biomol NMR, 37, 43-51.  
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
16767502 C.Schmitz, M.John, A.Y.Park, N.E.Dixon, G.Otting, G.Pintacuda, and T.Huber (2006).
Efficient chi-tensor determination and NH assignment of paramagnetic proteins.
  J Biomol NMR, 35, 79-87.  
17001092 E.Ab, A.R.Atkinson, L.Banci, I.Bertini, S.Ciofi-Baffoni, K.Brunner, T.Diercks, V.Dötsch, F.Engelke, G.E.Folkers, C.Griesinger, W.Gronwald, U.Günther, M.Habeck, R.N.de Jong, H.R.Kalbitzer, B.Kieffer, B.R.Leeflang, S.Loss, C.Luchinat, T.Marquardsen, D.Moskau, K.P.Neidig, M.Nilges, M.Piccioli, R.Pierattelli, W.Rieping, T.Schippmann, H.Schwalbe, G.Travé, J.Trenner, J.Wöhnert, M.Zweckstetter, and R.Kaptein (2006).
NMR in the SPINE Structural Proteomics project.
  Acta Crystallogr D Biol Crystallogr, 62, 1150-1161.  
16957918 F.Capozzi, F.Casadei, and C.Luchinat (2006).
EF-hand protein dynamics and evolution of calcium signal transduction: an NMR view.
  J Biol Inorg Chem, 11, 949-962.  
16981203 S.M.Mustafi, S.Mukherjee, K.V.Chary, and G.Cavallaro (2006).
Structural basis for the observed differential magnetic anisotropic tensorial values in calcium binding proteins.
  Proteins, 65, 656-669.
PDB codes: 2ev7 2i18
16094696 I.Bertini, C.Luchinat, G.Parigi, and R.Pierattelli (2005).
NMR spectroscopy of paramagnetic metalloproteins.
  Chembiochem, 6, 1536-1549.  
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 code is shown on the right.

 

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