3VYK

Crystal structure of C-type lectin domain of murine dendritic cell inhibitory receptor 2 in complex with N-glycan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Recognition of Bisecting N-Acetylglucosamine: STRUCTURAL BASIS FOR ASYMMETRIC INTERACTION WITH THE MOUSE LECTIN DENDRITIC CELL INHIBITORY RECEPTOR 2

Nagae, M.Yamanaka, K.Hanashima, S.Ikeda, A.Morita-Matsumoto, K.Satoh, T.Matsumoto, N.Yamamoto, K.Yamaguchi, Y.

(2013) J Biol Chem 288: 33598-33610

  • DOI: https://doi.org/10.1074/jbc.M113.513572
  • Primary Citation of Related Structures:  
    3VYJ, 3VYK

  • PubMed Abstract: 

    Dendritic cell inhibitory receptor 2 (DCIR2) is a C-type lectin expressed on classical dendritic cells. We recently identified the unique ligand specificity of mouse DCIR2 (mDCIR2) toward biantennary complex-type glycans containing bisecting N-acetylglucosamine (GlcNAc). Here, we report the crystal structures of the mDCIR2 carbohydrate recognition domain in unliganded form as well as in complex with an agalactosylated complex-type N-glycan unit carrying a bisecting GlcNAc residue. Bisecting GlcNAc and the α1-3 branch of the biantennary oligosaccharide asymmetrically interact with canonical and non-canonical mDCIR2 residues. Ligand-protein interactions occur directly through mDCIR2-characteristic amino acid residues as well as via a calcium ion and water molecule. Our structural and biochemical data elucidate for the first time the unique binding mode of mDCIR2 for bisecting GlcNAc-containing glycans, a mode that contrasts sharply with that of other immune C-type lectin receptors such as DC-SIGN.


  • Organizational Affiliation

    Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-type lectin domain family 4, member a4129Mus musculusMutation(s): 0 
Gene Names: Dcir2
UniProt & NIH Common Fund Data Resources
Find proteins for Q5YIR8 (Mus musculus)
Explore Q5YIR8 
Go to UniProtKB:  Q5YIR8
IMPC:  MGI:3624119
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5YIR8
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]methyl alpha-D-mannopyranoside
B
6N/A
Glycosylation Resources
GlyTouCan:  G81550YZ
GlyCosmos:  G81550YZ
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.341α = 90
b = 76.341β = 90
c = 50.556γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-16
    Changes: Database references
  • Version 1.2: 2013-12-11
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary