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⇱ RCSB PDB - 5B1W: Crystal structure of human dendritic cell inhibitory receptor (DCIR) C-type lectin domain in ligand-free form

πŸ‘ RCSB PDB
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Structures from the PDB archive		1,062,058
Computed Structure Models (CSM)

 5B1W | pdb_00005b1w

Crystal structure of human dendritic cell inhibitory receptor (DCIR) C-type lectin domain in ligand-free form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Γ…
  • R-Value Free: 
    0.284 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.253 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 
    0.254 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of human dendritic cell inhibitory receptor C-type lectin domain reveals the binding mode with N-glycan

Nagae, M., Ikeda, A., Hanashima, S., Kojima, T., Matsumoto, N., Yamamoto, K., Yamaguchi, Y.

(2016) FEBS Lett 590: 1280-1288

  • DOI: https://doi.org/10.1002/1873-3468.12162
  • Primary Citation Related Structures: 
    5B1W, 5B1X

  • PubMed Abstract: 

    Human dendritic cell inhibitory receptor (DCIR) is a C-type lectin receptor expressed in classical dendritic cells and accepts several oligosaccharide ligands including N-glycans. Here, we report the crystal structures of human DCIR C-type lectin domains in the absence and presence of a branched N-glycan unit. The domain has a typical C-type lectin fold and two bound calcium ions. In the ligand-bound form, the disaccharide unit (GlcNAcΞ²1-2Man) acceptably fits the electron density map, indicating that it forms the main epitope. The recognition of the nonterminal N-glycan unit explains the relatively broad specificity of this lectin.

    • Organizational Affiliation: 
    • Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, Wako, Saitama, Japan.
    • Department of Chemistry, Osaka University, Machikaneyama, Toyonaka, Osaka, Japan.
    • Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

Macromolecule Content 

  • Total Structure Weight: 63.57 kDa 
  • Atom Count: 4,301 
  • Modeled Residue Count: 516 
  • Deposited Residue Count: 536 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C-type lectin domain family 4 member A
A, B, C, D
134Homo sapiensMutation(s): 0 
Gene Names: CLEC4A, CLECSF6, DCIR, LLIR, HDCGC13P
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UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMR7 (Homo sapiens)
Explore Q9UMR7 
Go to UniProtKB:  Q9UMR7
PHAROS:  Q9UMR7
GTEx:  ENSG00000111729 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UMR7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Γ…
  • R-Value Free:  0.284 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.253 (Depositor), 0.256 (DCC) 
  • R-Value Observed: 0.254 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Γ… )Angle ( ˚ )
a = 102.489Ξ± = 90
b = 105.832Ξ² = 90
c = 65.387Ξ³ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
MEXTJapan24770111
MEXTJapan15K18496

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.