1WMY

Crystal Structure of C-type Lectin CEL-I from Cucumaria echinata

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Characteristic Recognition of N-Acetylgalactosamine by an Invertebrate C-type Lectin, CEL-I, Revealed by X-ray Crystallographic Analysis

Sugawara, H., Kusunoki, M., Kurisu, G., Fujimoto, T., Aoyagi, H., Hatakeyama, T.

(2004) J.Biol.Chem. 279: 45219-45225

  • DOI: 10.1074/jbc.M408840200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • CEL-I is a C-type lectin, purified from the sea cucumber Cucumaria echinata, that shows a high specificity for N-acetylgalactosamine (GalNAc). We determined the crystal structures of CEL-I and its complex with GalNAc at 2.0 and 1.7 A resolution, resp ...

    CEL-I is a C-type lectin, purified from the sea cucumber Cucumaria echinata, that shows a high specificity for N-acetylgalactosamine (GalNAc). We determined the crystal structures of CEL-I and its complex with GalNAc at 2.0 and 1.7 A resolution, respectively. CEL-I forms a disulfide-linked homodimer and contains two intramolecular disulfide bonds, although it lacks one intramolecular disulfide bond that is widely conserved among various C-type carbohydrate recognition domains (CRDs). Although the sequence similarity of CEL-I with other C-type CRDs is low, the overall folding of CEL-I was quite similar to those of other C-type CRDs. The structure of the complex with GalNAc revealed that the basic recognition mode of GalNAc was very similar to that for the GalNAc-binding mutant of the mannose-binding protein. However, the acetamido group of GalNAc appeared to be recognized more strongly by the combination of hydrogen bonds to Arg115 and van der Waals interaction with Gln70. Mutational analyses, in which Gln70 and/or Arg115 were replaced by alanine, confirmed that these residues contributed to GalNAc recognition in a cooperative manner.

    Related Citations: 
    • Crystallization and Preliminary Crystallographic Study of an Invertebrate C-type Lectin, CEL-I, from the Marine Invertebrate Cucumaria echinata
      Hatakeyama, T.,Matsuo, N.,Aoyagi, H.,Sugawara, H.,Uchida, T.,Kurisu, G.,Kusunoki, M.
      (2002) Acta Crystallogr.,Sect.D 58: 143

    Organizational Affiliation: 

    Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
lectin CEL-I, N-acetyl-D-galactosamine-specific C-type
A, B
140Cucumaria echinataMutation(s): 0 
Find proteins for Q7M462 (Cucumaria echinata)
Go to UniProtKB:  Q7M462
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD
Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.138 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.380α = 90.00
b = 69.940β = 136.46
c = 76.690γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
REFMACrefinement
DPSdata reduction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance