PDBsum entry 1odb

Metal binding protein

PDB id: 1odb

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.Wilson, 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

Protein chains

P80511  (S10AC_HUMAN) -  Protein S100-A12 from Homo sapiens

Seq: 92 a.a.

Struc: 91 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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 Å) and for data set II ( [II] = 1.65 Å). (b) Anomalous difference electron-density maps for data sets I ( = 1.37 Å) and II ( = 1.65 Å). 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.