1N47

Isolectin B4 from Vicia villosa in complex with the Tn antigen

• PDB DOI: https://doi.org/10.2210/pdb1N47/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Vicia villosa
• Mutation(s): No 


• Deposited: 2002-10-30 Released: 2003-02-25 
• Deposition Author(s): Babino, A., Tello, D., Rojas, A., Bay, S., Osinaga, E., Alzari, P.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.238 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

The crystal structure of a plant lectin in complex with the Tn antigen

Babino, A., Tello, D., Rojas, A., Bay, S., Osinaga, E., Alzari, P.M.

(2003) FEBS Lett 536: 106-110

• PubMed: 12586347 
• DOI: https://doi.org/10.1016/s0014-5793(03)00037-1
• Primary Citation of Related Structures:  
  1N47


• PubMed Abstract: 
  

  The structure of the tetrameric Vicia villosa isolectin B4 (VVLB4) in complex with a cancer antigen, the Tn glycopeptide (GalNAc-O-Ser), was determined at 2.7 A resolution. The N-acetylgalactoside moiety of the ligand binds to the primary combining site of VVLB4 in a similar way as observed for other Gal/GalNAc-specific plant lectins. The amino acid moiety of the Tn antigen is largely exposed to the solvent and makes few contacts with the protein. The structure of the complex provides a framework to understand the differences in the strength of VVLB4 binding to different sugars and emphasizes the role of a single protein residue, Tyr127, as a structural determinant of Tn-binding specificity.

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Organizational Affiliation: 

Departamento de Bioquimica, Facultad de Medicina, Av. Gral Flores 2125, Montevideo, Uruguay.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 102.81 kDa 
• Atom Count: 7,293 
• Modelled Residue Count: 932 
• Deposited Residue Count: 932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isolectin B4	A, B, C, D	233	Vicia villosa	Mutation(s): 0
UniProt
Find proteins for P56625 (Vicia villosa) Explore P56625  Go to UniProtKB:  P56625
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G11971MR GlyCosmos:  G11971MR GlyGen:  G11971MR

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2G	L [auth A], P [auth B], T [auth C], X [auth D]	2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N
SER	K [auth A], O [auth B], S [auth C], W [auth D]	SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N
MN	J [auth A], N [auth B], R [auth C], V [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA	I [auth A], M [auth B], Q [auth C], U [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.238 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.51	α = 90
b = 85.51	β = 90
c = 153.65	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-25 
Deposition Author(s): Babino, A., Tello, D., Rojas, A., Bay, S., Osinaga, E., Alzari, P.M.

Revision History  

• Version 1.0: 2003-02-25
  Type: Initial release
  
• Version 1.1: 2008-04-02
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-04-03
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary