2WC8

S100A12 complex with zinc in the absence of calcium

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

The Crystal Structures of Human S100A12 in Apo Form and in Complex with Zinc: New Insights Into S100A12 Oligomerisation.

Moroz, O.V., Blagova, E.V., Wilkinson, A.J., Wilson, K.S., Bronstein, I.B.

(2009) J.Mol.Biol. 391: 536

  • DOI: 10.1016/j.jmb.2009.06.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The functions of the members of the S100 family of EF-hand proteins are modulated by calcium and, in a number of cases, by zinc or copper. One such protein is S100A12, which is implicated in inflammation and host-parasite responses. Previously, we re ...

    The functions of the members of the S100 family of EF-hand proteins are modulated by calcium and, in a number of cases, by zinc or copper. One such protein is S100A12, which is implicated in inflammation and host-parasite responses. Previously, we reported the structures of human S100A12 in both low (dimeric) and high (hexameric) calcium forms and, in addition, that of a complex with copper and calcium. Here we report the crystal structures of the metal-free apo form of human S100A12 at 1.77 A resolution and of the zinc complex in two crystal forms (P2(1)2(1)2(1) and F222) to 1.88 A and 1.73 A resolution, respectively. These are the first structures of a zinc-only complex of an S100 protein to be determined. The zinc complex structure shows significant differences from those of both calcium-loaded and apo-S100A12 structures, and comparisons suggest an explanation for the zinc-induced 1500-fold increase in calcium affinity. In addition, the new structures provide insight into the role of zinc-calcium interplay in the transition of S100A12 from a dimer through a tetramer to a hexamer. The role of both zinc and calcium in target binding by S100A12 during host-parasite responses is confirmed by experiments with paramyosin from the tropical parasites Onchocerca volvulus and Brugia malayi.

    Related Citations: 
    • The Structure of S100A12 in a Hexameric Form and its Proposed Role in Receptor Signalling.
      Moroz, O.V.,Antson, A.A.,Dodson, E.J.,Burrell, H.J.,Grist, S.J.,Lloyd, R.M.,Maitland, N.J.,Dodson, G.G.,Wilson, K.S.,Lukanidin, E.,Bronstein, I.B.
      (2002) Acta Crystallogr.,Sect.D 58: 407
    • The Three-Dimensional Structure of Human S100A12.
      Moroz, O.V.,Antson, A.A.,Murshudov, G.N.,Maitland, N.J.,Dodson, G.G.,Wilson, K.S.,Skibshoj, I.,Lukanidin, E.M.,Bronstein, I.B.
      (2001) Acta Crystallogr.,Sect.D 57: 20
    • Structure of the Human S100A12-Copper Complex: Implications for Host-Parasite Defence.
      Moroz, O.V.,Antson, A.A.,Grist, S.J.,Maitland, N.J.,Dodson, G.G.,Wilson, K.S.,Lukanidin, E.,Bronstein, I.B.
      (2003) Acta Crystallogr.,Sect.D 59: 859

    Organizational Affiliation: 

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK. olga@ysbl.york.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN S100-A12
A, B, C, D
95Homo sapiensMutation(s): 0 
Gene Names: S100A12
Find proteins for P80511 (Homo sapiens)
Go to Gene View: S100A12
Go to UniProtKB:  P80511
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA
Download SDF File 
Download CCD File 
A, B, C, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT
Download SDF File 
Download CCD File 
C
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.991α = 90.00
b = 81.830β = 90.00
c = 85.725γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
MOLREPphasing
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance