6RYM

Structure of carbohydrate recognition domain with GlcNAc bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Atomic-resolution crystal structures of the immune protein conglutinin from cow reveal specific interactions of its binding site withN-acetylglucosamine.

Paterson, J.M.Shaw, A.J.Burns, I.Dodds, A.W.Prasad, A.Reid, K.B.Greenhough, T.J.Shrive, A.K.

(2019) J.Biol.Chem. --: --

  • DOI: 10.1074/jbc.RA119.010271
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bovine conglutinin is an immune protein that is involved in host resistance to microbes and parasites and interacts with complement component iC3b, agglutinates erythrocytes, and neutralizes influenza A virus. Here, we determined the high-resolution ...

    Bovine conglutinin is an immune protein that is involved in host resistance to microbes and parasites and interacts with complement component iC3b, agglutinates erythrocytes, and neutralizes influenza A virus. Here, we determined the high-resolution (0.97-1.46 Å) crystal structures with and without bound ligand of a recombinant fragment of conglutinin's C-terminal carbohydrate-recognition domain (CRD). The structures disclosed that the high-affinity ligand N -acetyl-D-glucosamine (GlcNAc) binds in the collectin CRD calcium site by interacting with the O3' and O4' hydroxyls alongside additional specific interactions of the N -acetyl group oxygen and nitrogen with Lys343 and Asp320, respectively. These residues, unique to conglutinin and differing both in sequence and location from those in other collectins, result in specific, high-affinity binding for GlcNAc. The binding pocket flanking residue Val339, unlike the equivalent Arg343 in the homologous human surfactant protein D, is sufficiently small to allow conglutinin Lys343 access to the bound ligand, whereas Asp320 lies in an extended loop proximal to the ligand-binding site and bounded at both ends by conserved residues that coordinate to both calcium and ligand. This loop becomes ordered on ligand binding. The electron density revealed both α and β anomers of GlcNAc, consistent with the added α/βGlcNAc mixture. Crystals soaked with α1-2 mannobiose, a putative component of iC3b, reported to bind to conglutinin, failed to reveal bound ligand, suggesting a requirement for presentation of mannobiose as part of an extended physiological ligand. These results reveal a highly specific GlcNAc-binding pocket in conglutinin and a novel collectin mode of carbohydrate recognition.


    Organizational Affiliation

    University of Oxford, United Kingdom.,Keele University.,Keele University, United Kingdom.,School of Life Sciences, Keele University, United Kingdom.,Department of Biochemistry, MRC Immunochemistry Unit, United Kingdom.,ISTM and School of Life Sciences, Keele University, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Conglutinin
A
128Bos taurusMutation(s): 0 
Gene Names: CGN1
Find proteins for P23805 (Bos taurus)
Go to UniProtKB:  P23805
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.161 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 50.225α = 90.00
b = 50.225β = 90.00
c = 51.925γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release