1EWC

CRYSTAL STRUCTURE OF ZN2+ LOADED STAPHYLOCOCCAL ENTEROTOXIN H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The crystal structure of staphylococcal enterotoxin H: implications for binding properties to MHC class II and TcR molecules.

Hakansson, M.Petersson, K.Nilsson, H.Forsberg, G.Bjork, P.Antonsson, P.Svensson, L.A.

(2000) J.Mol.Biol. 302: 527-537

  • DOI: 10.1006/jmbi.2000.4093
  • Primary Citation of Related Structures:  1ENF, 1F77

  • PubMed Abstract: 
  • The X-ray structure of the superantigen staphylococcal enterotoxin H (SEH) has been determined at 1.69 A resolution. In this paper we present two structures of zinc-free SEH (apoSEH) and one zinc-loaded form of SEH (ZnSEH). SEH exhibits the conventio ...

    The X-ray structure of the superantigen staphylococcal enterotoxin H (SEH) has been determined at 1.69 A resolution. In this paper we present two structures of zinc-free SEH (apoSEH) and one zinc-loaded form of SEH (ZnSEH). SEH exhibits the conventional superantigen (SAg) fold with two characteristic domains. In ZnSEH one zinc ion per SEH molecule is bound to the C-terminal beta-sheet in the region implicated for major histocompatibility complex class II (MHC class II) binding in SEA, SED and SEE. Surprisingly, the zinc ion has only two ligating amino acid residues His206 and Asp208. The other ligands to the zinc ion are two water molecules. An extensive packing interaction between two symmetry-related molecules in the crystal, 834 A(2)/molecule, forms a cavity that buries the zinc ions of the molecules. This dimer-like interaction is found in two crystal forms. Nevertheless, zinc-dependent dimerisation is not observed in solution, as seen in the case of SED. A unique feature of SEH as compared to other staphylococcal enterotoxins is a large negatively charged surface close to the Zn(2+) site. The interaction of SEH with MHC class II is the strongest known among the staphylococcal enterotoxins. However, SEH seems to lack a SEB-like MHC class II binding site, since the side-chain properties of structurally equivalent amino acid residues in SEH and those in SEB-binding MHC class II differ dramatically. There is also a structural flexibility between the domains of SEH. The domains of two apoSEH structures are related by a 5 degrees rotation leading to at most 3 A difference in C(alpha) positions. Since the T-cell receptor probably interacts with both domains, SEH by this rotation may modulate its binding to different TcR Vbeta-chains.


    Organizational Affiliation

    Molecular Biophysics, Centre for Chemistry and Chemical Engineering, Lund University, Lund, S-221 00, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENTEROTOXIN H
A
214Staphylococcus aureusGene Names: entH (seh)
Find proteins for P0A0M0 (Staphylococcus aureus)
Go to UniProtKB:  P0A0M0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.230 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 86.380α = 90.00
b = 86.380β = 90.00
c = 228.790γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
TRUNCATEdata reduction
XDSdata scaling
XDSdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-10-04
    Type: Data collection, Refinement description