1TL2

TACHYLECTIN-2 FROM TACHYPLEUS TRIDENTATUS (JAPANESE HORSESHOE CRAB)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Tachylectin-2: crystal structure of a specific GlcNAc/GalNAc-binding lectin involved in the innate immunity host defense of the Japanese horseshoe crab Tachypleus tridentatus.

Beisel, H.G.Kawabata, S.Iwanaga, S.Huber, R.Bode, W.

(1999) EMBO J. 18: 2313-2322

  • DOI: 10.1093/emboj/18.9.2313

  • PubMed Abstract: 
  • Tachylectin-2, isolated from large granules of the hemocytes of the Japanese horseshoe crab (Tachypleus tridentatus), is a 236 amino acid protein belonging to the lectins. It binds specifically to N-acetylglucosamine and N-acetylgalactosamine and is ...

    Tachylectin-2, isolated from large granules of the hemocytes of the Japanese horseshoe crab (Tachypleus tridentatus), is a 236 amino acid protein belonging to the lectins. It binds specifically to N-acetylglucosamine and N-acetylgalactosamine and is a part of the innate immunity host defense system of the horseshoe crab. The X-ray structure of tachylectin-2 was solved at 2.0 A resolution by the multiple isomorphous replacement method and this molecular model was employed to solve the X-ray structure of the complex with N-acetylglucosamine. Tachylectin-2 is the first protein displaying a five-bladed beta-propeller structure. Five four-stranded antiparallel beta-sheets of W-like topology are arranged around a central water-filled tunnel, with the water molecules arranged as a pentagonal dodecahedron. Tachylectin-2 exhibits five virtually identical binding sites, one in each beta-sheet. The binding sites are located between adjacent beta-sheets and are made by a large loop between the outermost strands of the beta-sheets and the connecting segment from the previous beta-sheet. The high number of five binding sites within the single polypeptide chain strongly suggests the recognition of carbohydrate surface structures of pathogens with a fairly high ligand density. Thus, tachylectin-2 employs strict specificity for certain N-acetyl sugars as well as the surface ligand density for self/non-self recognition.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, 82152 Martinsried, Germany. beisel@biochem.mpg.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (TACHYLECTIN-2)
A
236Tachypleus tridentatusMutation(s): 0 
Find proteins for Q27084 (Tachypleus tridentatus)
Go to UniProtKB:  Q27084
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NDGKd: 51280 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.162 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.460α = 90.00
b = 89.460β = 90.00
c = 73.620γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SHELXL-97phasing
CCP4model building
CCP4data scaling
CCP4phasing
SHARPphasing
SHELXL-97model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-15
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description