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PDBsum entry 1y1a

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protein ligands metals Protein-protein interface(s) links
Metal binding protein PDB id
1y1a
Jmol
Contents
Protein chain
183 a.a. *
Ligands
GSH
Metals
_CA ×6
Waters ×278
* Residue conservation analysis
PDB id:
1y1a
Name: Metal binding protein
Title: Crystal structure of calcium and integrin binding protein
Structure: Calcium and integrin binding 1 (calmyrin). Chain: a, b. Synonym: cib1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: cib1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Resolution:
2.30Å     R-factor:   0.236     R-free:   0.251
Authors: C.J.Blamey,C.Ceccarelli,U.P.Naik,B.J.Bahnson
Key ref:
C.J.Blamey et al. (2005). The crystal structure of calcium- and integrin-binding protein 1: insights into redox regulated functions. Protein Sci, 14, 1214-1221. PubMed id: 15840829 DOI: 10.1110/ps.041270805
Date:
17-Nov-04     Release date:   03-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
Q99828  (CIB1_HUMAN) -  Calcium and integrin-binding protein 1
Seq:
Struc:
191 a.a.
183 a.a.
Key:    Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell periphery   24 terms 
  Biological process     response to ischemia   45 terms 
  Biochemical function     protein binding     5 terms  

 

 
DOI no: 10.1110/ps.041270805 Protein Sci 14:1214-1221 (2005)
PubMed id: 15840829  
 
 
The crystal structure of calcium- and integrin-binding protein 1: insights into redox regulated functions.
C.J.Blamey, C.Ceccarelli, U.P.Naik, B.J.Bahnson.
 
  ABSTRACT  
 
Calcium- and integrin-binding protein 1 (CIB1) is involved in the process of platelet aggregation by binding the cytoplasmic tail of the alpha(IIb) subunit of the platelet-specific integrin alpha(Iib)beta(3). Although poorly understood, it is widely believed that CIB1 acts as a global signaling regulator because it is expressed in many tissues that do not express integrin alpha(Iib)beta(3). We report the structure of human CIB1 to a resolution of 2.3 A, crystallized as a dimer. The dimer interface includes an extensive hydrophobic patch in a crystal form with 80% solvent content. Although the dimer form of CIB1 may not be physiologically relevant, this intersub-unit surface is likely to be linked to alpha(IIb) binding and to the binding of other signaling partner proteins. The C-terminal domain of CIB1 is structurally similar to other EF-hand proteins such as calmodulin and calcineurin B. Despite structural homology to the C-terminal domain, the N-terminal domain of CIB1 lacks calcium-binding sites. The structure of CIB1 revealed a complex with a molecule of glutathione in the reduced state bond to the N-terminal domain of one of the two subunits poised to interact with the free thiol of C35. Glutathione bound in this fashion suggests CIB1 may be redox regulated. Next to the bound GSH, the orientation of residues C35, H31, and S48 is suggestive of a cysteine-type protein phosphatase active site. The potential enzymatic activity of CIB1 is discussed and suggests a mechanism by which it regulates a wide variety of proteins in cells in addition to platelets.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The structure of Ca^2+-CIB1. (A) CIB1 crystallized as a homodimer in the asymmetric unit with chain A (yellow) and chain B (blue) complexed to two Ca^2+ atoms (gray) in the EF-hands 3 and 4. The N and C terminus of chain A are labeled in red. Chain B has a bound GSH (green) in the reduced form. The subunits are oriented in a head-to-tail fashion with the N-terminal domain of one chain interacting with the C-terminal domain of the neighboring chain. (B) The subunit interface of chain A is rotated toward the viewer displaying in purple ball and stick a hydrophobic patch of the C-terminal domain on the right (I106, Y110, I114, F115, F117, A184, F187) and the N-terminal domain on the left (F21, F69, I73, V76, F77, V97, F98, P104). Also shown in the N-terminal domain is a patch of negative charged residues in red ball and stick (E89, E90, E93). (C) The electrostatic potential of the subunit interface surface of chain A is displayed in the identical view to B using the program GRASP (Honig and Nicholls 1995). The surface is colored according to convention with red indicating negative charge, blue positive charge, and white net neutral charge. The electrostatic potential surface further highlights the hydrophobic patch of the N- and C-terminal domains, as well as the same negative patch indicated in B of the N-terminal domain surface.
 
  The above figure is reprinted by permission from the Protein Society: Protein Sci (2005, 14, 1214-1221) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19388079 A.P.Yamniuk, K.L.Anderson, M.E.Fraser, and H.J.Vogel (2009).
Auxiliary Ca2+ binding sites can influence the structure of CIB1.
  Protein Sci, 18, 1128-1134.  
17414216 T.M.Leisner, W.Yuan, J.C.DeNofrio, J.Liu, and L.V.Parise (2007).
Tickling the tails: cytoplasmic domain proteins that regulate integrin alphaIIbbeta3 activation.
  Curr Opin Hematol, 14, 255-261.  
  16820687 C.J.Jackson, P.D.Carr, H.K.Kim, J.W.Liu, and D.L.Ollis (2006).
The purification, crystallization and preliminary diffraction of a glycerophosphodiesterase from Enterobacter aerogenes.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 659-661.  
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.