1M26

Crystal structure of jacalin-T-antigen complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexs

Jeyaprakash, A.A.Rani, P.G.Reddy, G.B.Banumathi, S.Betzel, C.Surolia, A.Vijayan, M.

(2002) J.Mol.Biol. 321: 637-645

  • Also Cited By: 1WS4, 1WS5, 4R6N, 4R6O, 4R6P, 4R6Q, 4R6R

  • PubMed Abstract: 
  • Thomsen-Friedenreich antigen (Galbeta1-3GalNAc), generally known as T-antigen, is expressed in more than 85% of human carcinomas. Therefore, proteins which specifically bind T-antigen have potential diagnostic value. Jacalin, a lectin from jack fruit ...

    Thomsen-Friedenreich antigen (Galbeta1-3GalNAc), generally known as T-antigen, is expressed in more than 85% of human carcinomas. Therefore, proteins which specifically bind T-antigen have potential diagnostic value. Jacalin, a lectin from jack fruit (Artocarpus integrifolia) seeds, is a tetramer of molecular mass 66kDa. It is one of the very few proteins which are known to bind T-antigen. The crystal structure of the jacalin-T-antigen complex has been determined at 1.62A resolution. The interactions of the disaccharide at the binding site are predominantly through the GalNAc moiety, with Gal interacting only through water molecules. They include a hydrogen bond between the anomeric oxygen of GalNAc and the pi electrons of an aromatic side-chain. Several intermolecular interactions involving the bound carbohydrate contribute to the stability of the crystal structure. The present structure, along with that of the Me-alpha-Gal complex, provides a reasonable qualitative explanation for the known affinities of jacalin to different carbohydrate ligands and a plausible model of the binding of the lectin to T-antigen O-linked to seryl or threonyl residues. Including the present one, the structures of five lectin-T-antigen complexes are available. GalNAc occupies the primary binding site in three of them, while Gal occupies the site in two. The choice appears to be related to the ability of the lectin to bind sialylated sugars. In either case, most of the lectin-disaccharide interactions are at the primary binding site. The conformation of T-antigen in the five complexes is nearly the same.


    Related Citations: 
    • A novel mode of carbohydrate recognition in jacalin, a Moraceae plant lectin with a beta-prism fold
      Sankaranarayanan, R,Sekar, K.,Banerjee, R.,Sharma, V.,Surolia, A.,Vijayan, M.
      (1996) Nat.Struct.Mol.Biol. 3: 596


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, UGC Centre of Advanced Science, Bangalore, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Jacalin, alpha chain
A, C, E, G
133Artocarpus integerN/A
Find proteins for P18670 (Artocarpus integer)
Go to UniProtKB:  P18670
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Jacalin, beta chain
B, D, F, H
17Artocarpus integerN/A
Find proteins for P18673 (Artocarpus integer)
Go to UniProtKB:  P18673
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, C, E, G
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
A2G
Query on A2G

Download SDF File 
Download CCD File 
A, C, E, G
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.920α = 90.00
b = 78.000β = 100.73
c = 67.910γ = 90.00
Software Package:
Software NamePurpose
AUTOMARdata reduction
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-12
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description