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PDBsum entry 1odb

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protein metals Protein-protein interface(s) links
Metal-binding protein PDB id
1odb
Jmol
Contents
Protein chain
(+ 0 more) 91 a.a. *
Metals
_CA ×12
_CU ×6
Waters ×370
* Residue conservation analysis
PDB id:
1odb
Name: Metal-binding protein
Title: The crystal structure of human s100a12 - copper complex
Structure: Calgranulin c. Chain: a, b, c, d, e, f. Synonym: s100a12, cagc, p6, cgrp, neutrophil s100 protein, calcium-binding protein in amniotic fluid 1, caaf1. Engineered: yes. Other_details: ca2+ and cu2+ bound form
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood. Cell: granulocyte. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.19Å     R-factor:   0.188     R-free:   0.226
Authors: O.V.Moroz,A.A.Antson,S.J.Grist,N.J.Maitland,G.G.Dodson,K.S.W E.M.Lukanidin,I.B.Bronstein
Key ref:
O.V.Moroz et al. (2003). Structure of the human S100A12-copper complex: implications for host-parasite defence. Acta Crystallogr D Biol Crystallogr, 59, 859-867. PubMed id: 12777802 DOI: 10.1107/S0907444903004700
Date:
15-Feb-03     Release date:   12-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P80511  (S10AC_HUMAN) -  Protein S100-A12
Seq:
Struc:
92 a.a.
91 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   7 terms 
  Biological process     immune system process   15 terms 
  Biochemical function     protein binding     6 terms  

 

 
DOI no: 10.1107/S0907444903004700 Acta Crystallogr D Biol Crystallogr 59:859-867 (2003)
PubMed id: 12777802  
 
 
Structure of the human S100A12-copper complex: implications for host-parasite defence.
O.V.Moroz, A.A.Antson, S.J.Grist, N.J.Maitland, G.G.Dodson, K.S.Wilson, E.Lukanidin, I.B.Bronstein.
 
  ABSTRACT  
 
S100A12 is a member of the S100 family of EF-hand calcium-modulated proteins. Together with S100A8 and S100A9, it belongs to the calgranulin subfamily, i.e. it is mainly expressed in granulocytes, although there is an increasing body of evidence of expression in keratinocytes and psoriatic lesions. As well as being linked to inflammation, allergy and neuritogenesis, S100A12 is involved in host-parasite response, as are the other two calgranulins. Recent data suggest that the function of the S100-family proteins is modulated not only by calcium, but also by other metals such as zinc and copper. Previously, the structure of human S100A12 in low-calcium and high-calcium structural forms, crystallized in space groups R3 and P2(1), respectively, has been reported. Here, the structure of S100A12 in complex with copper (space group P2(1)2(1)2; unit-cell parameters a = 70.6, b = 119.0, c = 90.2 A) refined at 2.19 A resolution is reported. Comparison of anomalous difference electron-density maps calculated with data collected with radiation of wavelengths 1.37 and 1.65 A shows that each monomer binds a single copper ion. The copper binds at an equivalent site to that at which another S100 protein, S100A7, binds zinc. The results suggest that copper binding may be essential for the functional role of S100A12 and probably the other calgranulins in the early immune response.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 (a) ( ) plots for copper (in blue) and for calcium (in red). Dotted lines correspond to the wavelengths for set I ( [I] = 1.37 ) and for data set II ( [II] = 1.65 ). (b) Anomalous difference electron-density maps for data sets I ( = 1.37 ) and II ( = 1.65 ). Electron density for data set I is contoured at the 10 level and is shown in red. Electron density for data set II is contoured at the 5 level and is shown in green. This figure and Fig. 4-were generated using QUANTA (Molecular Simulations, Inc.).
Figure 6.
Figure 6 Superposition of the copper-binding site of S100A12 (PDB code [287]1odb ), the zinc-binding site of S100A7 ([288]2psr ) and corresponding regions of S100A8 ([289]1mr8 ), S100A9 ([290]1irj ) and S100B ([291]1mho ) shown in ball-and-stick representation. S100A12 is shown in blue, S100A8 in green, S100A9 in orange, S100A7 in yellow and S100B in violet. Copper ion from the S100A12-copper complex structure is in blue, zinc ion from the S100A7-zinc complex is in yellow. The figure was generated using MOLSCRIPT (Kraulis, 1991[292] [Kraulis, P. (1991). J. Appl. Cryst. 24, 946-950.]-[293][bluearr.gif] ) and Raster3D (Merritt & Murphy, 1994[294] [Merritt, E. A. & Murphy, M. E. P. (1994). Acta Cryst. D50, 869-873.]-[295][bluearr.gif] ).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2003, 59, 859-867) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21377473 M.Unno, T.Kawasaki, H.Takahara, C.W.Heizmann, and K.Kizawa (2011).
Refined crystal structures of human Ca(2+)/Zn(2+)-binding S100A3 protein characterized by two disulfide bridges.
  J Mol Biol, 408, 477-490.
PDB codes: 3nsi 3nsk 3nsl 3nso
20950652 T.Ostendorp, J.Diez, C.W.Heizmann, and G.Fritz (2011).
The crystal structures of human S100B in the zinc- and calcium-loaded state at three pH values reveal zinc ligand swapping.
  Biochim Biophys Acta, 1813, 1083-1091.
PDB codes: 3czt 3d0y 3d10
21262274 Z.Grabarek (2011).
Insights into modulation of calcium signaling by magnesium in calmodulin, troponin C and related EF-hand proteins.
  Biochim Biophys Acta, 1813, 913-921.  
20977662 G.Fritz, H.M.Botelho, L.A.Morozova-Roche, and C.M.Gomes (2010).
Natural and amyloid self-assembly of S100 proteins: structural basis of functional diversity.
  FEBS J, 277, 4578-4590.  
20015678 T.E.Kehl-Fie, and E.P.Skaar (2010).
Nutritional immunity beyond iron: a role for manganese and zinc.
  Curr Opin Chem Biol, 14, 218-224.  
18443896 J.Pietzsch, and S.Hoppmann (2009).
Human S100A12: a novel key player in inflammation?
  Amino Acids, 36, 381-389.  
  20523765 K.Hsu, C.Champaiboon, B.D.Guenther, B.S.Sorenson, A.Khammanivong, K.F.Ross, C.L.Geczy, and M.C.Herzberg (2009).
ANTI-INFECTIVE PROTECTIVE PROPERTIES OF S100 CALGRANULINS.
  Antiinflamm Antiallergy Agents Med Chem, 8, 290-305.  
19386136 O.V.Moroz, W.Burkitt, H.Wittkowski, W.He, A.Ianoul, V.Novitskaya, J.Xie, O.Polyakova, I.K.Lednev, A.Shekhtman, P.J.Derrick, P.Bjoerk, D.Foell, and I.B.Bronstein (2009).
Both Ca2+ and Zn2+ are essential for S100A12 protein -oligomerization and function.
  BMC Biochem, 10, 11.  
18602402 T.H.Charpentier, P.T.Wilder, M.A.Liriano, K.M.Varney, E.Pozharski, A.D.MacKerell, A.Coop, E.A.Toth, and D.J.Weber (2008).
Divalent metal ion complexes of S100B in the absence and presence of pentamidine.
  J Mol Biol, 382, 56-73.
PDB codes: 3cr2 3cr4 3cr5
17257225 A.Larsen, I.B.Bronstein, O.Dahl, T.Wentzel-Larsen, E.K.Kristoffersen, and M.K.Fagerhol (2007).
Quantification of S100A12 (EN-RAGE) in blood varies with sampling method, calcium and heparin.
  Scand J Immunol, 65, 192-201.  
16343958 A.J.Fielding, S.Fox, G.L.Millhauser, M.Chattopadhyay, P.M.Kroneck, G.Fritz, G.R.Eaton, and S.S.Eaton (2006).
Electron spin relaxation of copper(II) complexes in glassy solution between 10 and 120 K.
  J Magn Reson, 179, 92.  
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.