5F90

Crystal structure of a Crenomytilus grayanus lectin in complex with Gb3 allyl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.117 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Multivalent Marine Lectin from Crenomytilus grayanus Possesses Anti-cancer Activity through Recognizing Globotriose Gb3

Liao, J.-H.Chien, C.-T.Wu, H.-Y.Huang, K.-F.Wang, I.Ho, M.-R.Tu, I.-F.Lee, I.-M.Li, W.Shih, Y.-L.Wu, C.-Y.Lukyanov, P.A.Hsu, S.D.Wu, S.-H.

(2016) J.Am.Chem.Soc. 138: 4787-4795

  • DOI: 10.1021/jacs.6b00111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In this study, we report the structure and function of a lectin from the sea mollusk Crenomytilus grayanus collected from the sublittoral zone of Peter the Great Bay of the Sea of Japan. The crystal structure of C. grayanus lectin (CGL) was solved to ...

    In this study, we report the structure and function of a lectin from the sea mollusk Crenomytilus grayanus collected from the sublittoral zone of Peter the Great Bay of the Sea of Japan. The crystal structure of C. grayanus lectin (CGL) was solved to a resolution of 1.08 Å, revealing a β-trefoil fold that dimerizes into a dumbbell-shaped quaternary structure. Analysis of the crystal CGL structures bound to galactose, galactosamine, and globotriose Gb3 indicated that each CGL can bind three ligands through a carbohydrate-binding motif involving an extensive histidine- and water-mediated hydrogen bond network. CGL binding to Gb3 is further enhanced by additional side-chain-mediated hydrogen bonds in each of the three ligand-binding sites. NMR titrations revealed that the three binding sites have distinct microscopic affinities toward galactose and galactosamine. Cell viability assays showed that CGL recognizes Gb3 on the surface of breast cancer cells, leading to cell death. Our findings suggest the use of this lectin in cancer diagnosis and treatment.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica , Taipei 11529, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GalNAc/Gal-specific lectin
A, B
156Crenomytilus grayanusMutation(s): 0 
Find proteins for H2FH31 (Crenomytilus grayanus)
Go to UniProtKB:  H2FH31
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
LMR
Query on LMR

Download SDF File 
Download CCD File 
A
(2S)-2-hydroxybutanedioic acid
L-Malate
C4 H6 O5
BJEPYKJPYRNKOW-REOHCLBHSA-N
 Ligand Interaction
5VQ
Query on 5VQ

Download SDF File 
Download CCD File 
A, B
2-Propen-1-ol
allyl alcohol
C3 H6 O
XXROGKLTLUQVRX-UHFFFAOYSA-N
 Ligand Interaction
GLA
Query on GLA

Download SDF File 
Download CCD File 
A, B
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.117 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.043α = 90.00
b = 72.464β = 90.00
c = 94.361γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
SHELXCDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Council and Ministry of Science and TechnologyTaiwanNSC 100-2113-M-001-022-MY3, NSC 102-2811-M-001-132, MOST 103-2113-M-001-029-MY3, MOST 103-2811-M-001-126, NSC 103-2923-M-001-006-MY3, NSC 100-2113-M-001-031-MY2, NSC 102-2113-M-001-017-MY2

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references