4Q56

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


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 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Helix aspersa agglutinin (HAA)A101Cornu aspersumMutation(s): 0 
UniProt
Find proteins for A0A0R4I963 (Cornu aspersum)
Explore A0A0R4I963 
Go to UniProtKB:  A0A0R4I963
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseB6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G52988LW
GlyCosmos:  G52988LW
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A2G
Query on A2G

Download Ideal Coordinates CCD File 
D [auth A]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
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 = 47.9α = 90
b = 47.9β = 90
c = 281.53γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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