2YIP

Crystal Structure of Parasite Sarcocystis muris Microneme Protein SML- 2 in complex with 1-Thio-beta-D-Galactose (SPACEGROUP P212121)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Pan-Modular Structure of Microneme Protein Sml-2 from Parasite Sarcocystis Muris at 1.95 A Resolution and its Complex with 1-Thio-Beta-D-Galactose.

Mueller, J.J.Weiss, M.S.Heinemann, U.

(2011) Acta Crystallogr.,Sect.D D67: 936

  • DOI: 10.1107/S0907444911037796
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The microneme protein SML-2 is a member of a small family of galactose-specific lectins that play a role during host-cell invasion by the apicomplexan parasite Sarcocystis muris. The structures of apo SML-2 and the 1-thio-β-D-galactose-SML-2 complex ...

    The microneme protein SML-2 is a member of a small family of galactose-specific lectins that play a role during host-cell invasion by the apicomplexan parasite Sarcocystis muris. The structures of apo SML-2 and the 1-thio-β-D-galactose-SML-2 complex were determined at 1.95 and 2.1 Å resolution, respectively, by sulfur-SAD phasing. Highly elongated dimers are formed by PAN-domain tandems in the protomer, bearing the galactose-binding cavities at the distal apple-like domains. The detailed structure of the binding site in SML-2 explains the high specificity of galactose-endgroup binding and the broader specificity of the related Toxoplasma gondii protein TgMIC4 towards galactose and glucose. A large buried surface of highly hydrophobic character and 24 intersubunit hydrogen bonds stabilize the dimers and half of the 12 disulfides per dimer are shielded from the solvent by the polypeptide chain, thereby enhancing the resistance of the parasite protein towards unfolding and proteolysis that allows it to survive within the intestinal tracts of the intermediate and final hosts.


    Organizational Affiliation

    Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MICRONEME ANTIGEN L2
A, B, C, D, E, F
138Sarcocystis murisMutation(s): 0 
Find proteins for P81860 (Sarcocystis muris)
Go to UniProtKB:  P81860
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C, E, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
YIO
Query on YIO

Download SDF File 
Download CCD File 
A, B, C, D, E, F
(2R,3R,4S,5R,6S)-2-(HYDROXYMETHYL)-6-SULFANYL-OXANE-3,4,5-TRIOL
C6 H12 O5 S
JUSMHIGDXPKSID-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.310α = 90.00
b = 130.000β = 90.00
c = 158.850γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2011-11-30
    Type: Database references
  • Version 1.2: 2019-01-30
    Type: Advisory, Data collection, Experimental preparation, Other
  • Version 1.3: 2019-02-06
    Type: Data collection, Experimental preparation