1WMZ

Crystal Structure of C-type Lectin CEL-I complexed with N-acetyl-D-galactosamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation 3D Report Full Report



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:  
    1WMZ, 1WMY

  • 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 D Biol Crystallogr 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
lectin CEL-I, N-acetyl-D-galactosamine-specific C-typeABCD140Cucumaria echinataMutation(s): 0 
Find proteins for Q7M462 (Cucumaria echinata)
Explore Q7M462 
Go to UniProtKB:  Q7M462
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGA
Query on NGA

Download CCD File 
A, C, D
2-acetamido-2-deoxy-beta-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
A2G
Query on A2G

Download CCD File 
B
2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.58α = 90
b = 52.24β = 91.66
c = 136.59γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary