5ID8 | pdb_00005id8

Crystal structure of CGL1 from Crassostrea gigas, ligand free form (CGL1/FREE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 
    0.220 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Identification, Characterization, and X-ray Crystallographic Analysis of a Novel Type of Mannose-Specific Lectin CGL1 from the Pacific Oyster Crassostrea gigas.

Unno, H.Matsuyama, K.Tsuji, Y.Goda, S.Hiemori, K.Tateno, H.Hirabayashi, J.Hatakeyama, T.

(2016) Sci Rep 6: 29135-29135

  • DOI: https://doi.org/10.1038/srep29135
  • Primary Citation Related Structures: 
    5ID8, 5IDA, 5IDB

  • PubMed Abstract: 

    A novel mannose-specific lectin, named CGL1 (15.5 kDa), was isolated from the oyster Crassostrea gigas. Characterization of CGL1 involved isothermal titration calorimetry (ITC), glycoconjugate microarray, and frontal affinity chromatography (FAC). This analysis revealed that CGL1 has strict specificity for the mannose monomer and for high mannose-type N-glycans (HMTGs). Primary structure of CGL1 did not show any homology with known lectins but did show homology with proteins of the natterin family. Crystal structure of the CGL1 revealed a unique homodimer in which each protomer was composed of 2 domains related by a pseudo two-fold axis. Complex structures of CGL1 with mannose molecules showed that residues have 8 hydrogen bond interactions with O1, O2, O3, O4, and O5 hydroxyl groups of mannose. The complex interactions that are not observed with other mannose-binding lectins revealed the structural basis for the strict specificity for mannose. These characteristics of CGL1 may be helpful as a research tool and for clinical applications.


  • Organizational Affiliation
    • Graduate School of Engineering, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.

Macromolecule Content 

  • Total Structure Weight: 62.31 kDa 
  • Atom Count: 5,057 
  • Modeled Residue Count: 568 
  • Deposited Residue Count: 572 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Natterin-3
A, B, C, D
143Magallana gigasMutation(s): 0 
UniProt
Find proteins for K1QRB6 (Magallana gigas)
Explore K1QRB6 
Go to UniProtKB:  K1QRB6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK1QRB6
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AYA
Query on AYA
A, B, C, D
L-PEPTIDE LINKINGC5 H9 N O3ALA

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free:  0.220 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.596α = 90
b = 58.677β = 93.78
c = 107.927γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2016-06-29 
  • Deposition Author(s): Unno, H.

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Database references
  • Version 1.2: 2016-08-17
    Changes: Derived calculations
  • Version 1.3: 2020-02-19
    Changes: Data collection, Derived calculations
  • Version 1.4: 2025-04-09
    Changes: Data collection, Database references, Refinement description, Structure summary