6A56 | pdb_00006a56

AJLec from the Sea Anemone Anthopleura japonica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.176 (Depositor), 0.183 (DCC) 
  • R-Value Work: 
    0.142 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6A56

This is version 3.1 of the entry. See complete history

Literature

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 Related Structures: 
    6A56

  • 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.

Macromolecule Content 

  • Total Structure Weight: 38.04 kDa 
  • Atom Count: 3,090 
  • Modeled Residue Count: 328 
  • Deposited Residue Count: 328 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AJLec
A, B
164Anthopleura japonicaMutation(s): 0 
UniProt
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
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan: G84224TW
GlyCosmos: G84224TW
GlyGen: G84224TW

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.176 (Depositor), 0.183 (DCC) 
  • R-Value Work:  0.142 (Depositor), 0.151 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
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
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

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
  • Version 3.1: 2024-10-23
    Changes: Structure summary