Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.76 kDa 
• Atom Count: 1037 
• Residue Count: 101 
• Unique protein chains: 1

4Q56

Structure of Helix aspersa agglutinin with natural glycosylation and N-acetyl-alpha-D-galactosamine (GalNAc)

• DOI: 10.2210/pdb4Q56/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Cornu aspersum
• Mutation(s): No 


• Deposited: 2014-04-16 Released: 2015-10-14 
• Deposition Author(s): Pietrzyk, A.J., Bujacz, A., Bujacz, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.168 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 

Literature

Structural studies of Helix aspersa agglutinin complexed with GalNAc: A lectin that serves as a diagnostic tool.

Pietrzyk, A.J., Bujacz, A., Mak, P., Potempa, B., Niedziela, T.

(2015) Int J Biol Macromol 81: 1059-1068

• PubMed: 26416237 
• DOI: 10.1016/j.ijbiomac.2015.09.044
• Primary Citation of Related Structures:  
  4Q56


• PubMed Abstract: 
  

Lectins belong to a differentiated group of proteins known to possess sugar-binding properties. Due to this fact, they are interesting research targets in medical diagnostics. Helix aspersa agglutinin (HAA) is a lectin that recognizes the epitopes containing α-d-N-acetylgalactosamine (GalNAc), which is present at the surface of metastatic cancer cells. Although several reports have already described the use of HAA as a diagnostic tool, this protein was not characterized on the molecular level. Here, we present for the first time the structural information about lectin isolated from mucus of Helix aspersa (garden snail). The amino acid sequence of this agglutinin was determined by Edman degradation and tertiary as well as quaternary structure by X-ray crystallography. The high resolution crystal structure (1.38Å) and MALDI-TOF mass spectrometry analysis provide the detailed information about a large part of the HAA natural glycan chain. The topology of the GalNAc binding cleft and interaction with lectin are very well defined in the structure and fully confirmed by STD HSQC NMR spectroscopy. Together, this provides structural clues regarding HAA specificity and opens possibilities to rational modifications of this important diagnostic tool.

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Organizational Affiliation: 

Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, Wrocław 53-114, Poland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helix aspersa agglutinin (HAA)	A	101	Cornu aspersum	Mutation(s): 0
Find proteins for A0A0R4I963 (Cornu aspersum) Explore A0A0R4I963  Go to UniProtKB:  A0A0R4I963

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-L-fucopyranose-(1-3)-[beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	6		N-Glycosylation

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2G	A	2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 0.168 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.9	α = 90
b = 47.9	β = 90
c = 281.53	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-04-16 
• Released Date: 2015-10-14 
Deposition Author(s): Pietrzyk, A.J., Bujacz, A., Bujacz, G.

Revision History 

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 2.0: 2019-12-25
  Changes: Data collection, Derived calculations, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary