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PDBsum entry 1e8a

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protein metals Protein-protein interface(s) links
Antifungal protein PDB id
1e8a
Jmol
Contents
Protein chain
87 a.a. *
Metals
_CA ×4
Waters ×180
* Residue conservation analysis
PDB id:
1e8a
Name: Antifungal protein
Title: The three-dimensional structure of human s100a12
Structure: S100a12. Chain: a, b. Synonym: calgranulin c
Source: Homo sapiens. Human. Organism_taxid: 9606. Tissue: blood. Cell: granulocyte
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
1.95Å     R-factor:   0.180     R-free:   0.220
Authors: O.V.Moroz,A.A.Antson,G.N.Murshudov,N.J.Maitland,G.G.Dodson, K.S.Wilson,I.Skibshoj,E.M.Lukanidin,I.B.Bronstein
Key ref:
O.V.Moroz et al. (2001). The three-dimensional structure of human S100A12. Acta Crystallogr D Biol Crystallogr, 57, 20-29. PubMed id: 11134923 DOI: 10.1107/S090744490001458X
Date:
18-Sep-00     Release date:   08-Jan-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P80511  (S10AC_HUMAN) -  Protein S100-A12
Seq:
Struc:
92 a.a.
87 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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/S090744490001458X Acta Crystallogr D Biol Crystallogr 57:20-29 (2001)
PubMed id: 11134923  
 
 
The three-dimensional structure of human S100A12.
O.V.Moroz, A.A.Antson, G.N.Murshudov, N.J.Maitland, G.G.Dodson, K.S.Wilson, I.Skibshøj, E.M.Lukanidin, I.B.Bronstein.
 
  ABSTRACT  
 
The crystal structure of human EF-hand calcium-binding protein S100A12 in its calcium-bound form has been determined to 1.95 A resolution by molecular replacement using the structure of the S100B protein. The S100 family members are homologous to calmodulin and other related EF-hand calcium-binding proteins. Like the majority of S100 proteins, S100A12 is a dimer, with the interface between the two subunits being composed mostly of hydrophobic residues. The fold of S100A12 is similar to the other known crystal and solution structures of S100 proteins, except for the linker region between the two EF-hand motifs. Sequence and structure comparison between members of the S100 family suggests that the target-binding region in S100A12 is formed by the linker region and C-terminal residues of one subunit and the N-terminal residues of another subunit of the dimer. The N-terminal region of the target-binding site includes two glutamates that are conserved in most of the S100 sequences. The comparison also provided a better understanding of the role of the residues important for intra- and inter-subunit hydrophobic interactions. The precise role of S100A12 in cell behaviour is yet undefined, as is the case for the whole family, although it has been shown that the interaction of S100A12 with the RAGE receptor is implicated in inflammatory response.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Stereoview of the S100A12 dimer. Ribbons of the two monomers are in dark cyan and purple. Calcium ions are shown in red and the flexible linker loop in orange. This figure and Figs. 3-, 6-, 7-, 8-and 9-were generated using the program MOLSCRIPT (Kraulis, 1991[Kraulis, P. (1991). J. Appl. Cryst. 24, 946-950.]).
Figure 9.
Figure 9 Superposition of the N-terminal target-binding region of S100A10 (residues 1-12) bound to the annexin II peptide on the corresponding region of S100A12 (residues 1-12). Glutamates forming hydrogen bonds to the target and the corresponding residues of the target peptide are shown in ball-and-stick. The corresponding glutamates in the S100A12 structure are shown in ball-and-stick. S100A12 is shown in purple, S100A10 in yellow and annexin II peptide in green.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 20-29) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
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.  
  19890475 N.T.Wright, B.R.Cannon, D.B.Zimmer, and D.J.Weber (2009).
S100A1: Structure, Function, and Therapeutic Potential.
  Curr Chem Biol, 3, 138-145.  
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.  
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.  
17158877 J.Xie, D.S.Burz, W.He, I.B.Bronstein, I.Lednev, and A.Shekhtman (2007).
Hexameric calgranulin C (S100A12) binds to the receptor for advanced glycated end products (RAGE) using symmetric hydrophobic target-binding patches.
  J Biol Chem, 282, 4218-4231.  
16700049 C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.
  Proteins, 64, 404-421.  
  16682778 K.M.Boeshans, R.Wolf, C.Voscopoulos, W.Gillette, D.Esposito, T.C.Mueser, S.H.Yuspa, and B.Ahvazi (2006).
Purification, crystallization and preliminary X-ray diffraction of human S100A15.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 467-470.  
15927886 N.Leukert, C.Sorg, and J.Roth (2005).
Molecular basis of the complex formation between the two calcium-binding proteins S100A8 (MRP8) and S100A9 (MRP14).
  Biol Chem, 386, 429-434.  
15355353 T.Hatakeyama, M.Okada, S.Shimamoto, Y.Kubota, and R.Kobayashi (2004).
Identification of intracellular target proteins of the calcium-signaling protein S100A12.
  Eur J Biochem, 271, 3765-3775.  
12645004 J.C.Deloulme, B.J.Gentil, and J.Baudier (2003).
Monitoring of S100 homodimerization and heterodimeric interactions by the yeast two-hybrid system.
  Microsc Res Tech, 60, 560-568.  
12842036 S.Bhattacharya, and W.J.Chazin (2003).
Calcium-driven changes in S100A11 structure revealed.
  Structure, 11, 738-740.  
12645005 W.Nacken, J.Roth, C.Sorg, and C.Kerkhoff (2003).
S100A9/S100A8: Myeloid representatives of the S100 protein family as prominent players in innate immunity.
  Microsc Res Tech, 60, 569-580.  
12553726 C.Sopalla, N.Leukert, C.Sorg, and C.Kerkhoff (2002).
Evidence for the involvement of the unique C-tail of S100A9 in the binding of arachidonic acid to the heterocomplex S100A8/A9.
  Biol Chem, 383, 1895-1905.  
12045193 G.Fritz, P.R.Mittl, M.Vasak, M.G.Grutter, and C.W.Heizmann (2002).
The crystal structure of metal-free human EF-hand protein S100A3 at 1.7-A resolution.
  J Biol Chem, 277, 33092-33098.  
11937060 L.R.Otterbein, J.Kordowska, C.Witte-Hoffmann, C.L.Wang, and R.Dominguez (2002).
Crystal structures of S100A6 in the Ca(2+)-free and Ca(2+)-bound states: the calcium sensor mechanism of S100 proteins revealed at atomic resolution.
  Structure, 10, 557-567.
PDB codes: 1k8u 1k96 1k9k 1k9p
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.