AJLec from the Sea Anemone Anthopleura japonica

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

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This is version 3.0 of the entry. See complete history


Identification, Characterization, and X-ray Crystallographic Analysis of a Novel Type of Lectin AJLec from the Sea Anemone Anthopleura japonica.

Unno, H.Nakamura, A.Mori, S.Goda, S.Yamaguchi, K.Hiemori, K.Tateno, H.Hatakeyama, T.

(2018) Sci Rep 8: 11516-11516

  • DOI: https://doi.org/10.1038/s41598-018-29498-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A novel galactose-specific lectin, AJLec (18.5 kDa), was isolated from the sea anemone, Anthopleura japonica. AJLec was characterized using the hemagglutination assay, isothermal titration calorimetry (ITC), and glycoconjugate microarray analysis and we found that AJLec has a specificity for galactose monomers and β-linked terminal galactose residues in complex carbohydrates, but not for N-acetylgalactosamine (GalNAc), which is commonly recognized by galactose-binding lectins. The primary structure of AJLec did not show homology with known lectins, and a crystal structural analysis also revealed a unique homodimeric structure. The crystal structure of AJLec complexed with lactose was solved by measuring the sulfur single-wavelength anomalous diffraction (S-SAD) phasing with an in-house Cu Kα source method. This analysis revealed that the galactose residue in lactose was recognized via its O2, O3, and O4 hydroxyl groups and ring oxygen by calcium coordination and two hydrogen bonds with residues in the carbohydrate-binding site, which demonstrated strict specificity for the β-linked terminal galactose in this lectin.

  • Organizational Affiliation

    Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521, Japan. unno@nagasaki-u.ac.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
164Anthopleura japonicaMutation(s): 0 
Find proteins for A0A2Z5WLM1 (Anthopleura japonica)
Explore A0A2Z5WLM1 
Go to UniProtKB:  A0A2Z5WLM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2Z5WLM1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G84224TW
GlyCosmos:  G84224TW
GlyGen:  G84224TW
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.079α = 90
b = 79.732β = 90
c = 106γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan15K06977

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
  • Version 3.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary