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PDBsum entry 2k0j

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protein metals links
Metal binding protein PDB id
2k0j
Jmol
Contents
Protein chain
147 a.a. *
Metals
_LA
_CA ×3
* Residue conservation analysis
PDB id:
2k0j
Name: Metal binding protein
Title: Solution structure of cam complexed to drp1p
Structure: Calmodulin. Chain: a. Synonym: cam. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: calm1, calm, cam, cam1. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 1 models
Authors: I.Bertini,C.Luchinat,G.Parigi,J.Yuan,Structural Proteomics In Europe (Spine)
Key ref: I.Bertini et al. (2009). Accurate solution structures of proteins from X-ray data and a minimal set of NMR data: calmodulin-peptide complexes as examples. J Am Chem Soc, 131, 5134-5144. PubMed id: 19317469 DOI: 10.1021/ja8080764
Date:
04-Feb-08     Release date:   10-Mar-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P62158  (CALM_HUMAN) -  Calmodulin
Seq:
Struc:
149 a.a.
147 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   16 terms 
  Biological process     Fc-epsilon receptor signaling pathway   46 terms 
  Biochemical function     enzyme regulator activity     18 terms  

 

 
DOI no: 10.1021/ja8080764 J Am Chem Soc 131:5134-5144 (2009)
PubMed id: 19317469  
 
 
Accurate solution structures of proteins from X-ray data and a minimal set of NMR data: calmodulin-peptide complexes as examples.
I.Bertini, P.Kursula, C.Luchinat, G.Parigi, J.Vahokoski, M.Wilmanns, J.Yuan.
 
  ABSTRACT  
 
A strategy for the accurate determination of protein solution structures starting from X-ray data and a minimal set of NMR data is proposed and successfully applied to two complexes of calmodulin (CaM) with target peptides not previously described. Its implementation in the present case is based on the use of lanthanide ions as substitutes for calcium in one of the four calcium binding sites of CaM and the collection of pseudocontact shift (pcs) and residual dipolar coupling (rdc) restraints induced by the paramagnetic metals. Starting from the crystal structures, new structural models are calculated that are in excellent agreement with the paramagnetic restraints and differ significantly from the starting crystal structures. In particular, in both complexes, a change in orientation of the first helix of the N-terminal CaM domain and of the whole C-terminal domain is observed. The simultaneous use of paramagnetic pcs and rdc restraints has the following crucial advantages: (i) it allows one to assess the possible presence of interdomain conformational freedom, which cannot be detected if the rdc values are derived from external orienting media; (ii) in the absence of significant conformational freedom, the global orientation tensor can be independently and precisely determined from pcs values, which are less sensitive than rdc values to the presence of local structural inaccuracies, and therefore (iii) the relative rearrangement of a domain or a secondary structure element with respect to the metal-bearing domain can be detected.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20162649 B.Man, X.C.Su, H.Liang, S.Simonsen, T.Huber, B.A.Messerle, and G.Otting (2010).
3-Mercapto-2,6-pyridinedicarboxylic acid: a small lanthanide-binding tag for protein studies by NMR spectroscopy.
  Chemistry, 16, 3827-3832.  
20331317 B.Shapira, and J.H.Prestegard (2010).
Electron-nuclear interactions as probes of domain motion in proteins.
  J Chem Phys, 132, 115102.  
20429020 L.Duan, W.Liu, Z.J.Wang, A.H.Liang, and B.S.Yang (2010).
Critical role of tyrosine 79 in the fluorescence resonance energy transfer and terbium(III)-dependent self-assembly of ciliate Euplotes octocarinatus centrin.
  J Biol Inorg Chem, 15, 995.  
20300805 T.Saio, M.Yokochi, H.Kumeta, and F.Inagaki (2010).
PCS-based structure determination of protein-protein complexes.
  J Biomol NMR, 46, 271-280.
PDB code: 2ktr
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.