5B1W | pdb_00005b1w

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

• PDB DOI: https://doi.org/10.2210/pdb5B1W/pdb

• Classification: CARBOHYDRATE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-12-21 Released: 2016-05-11 
• Deposition Author(s): Nagae, M., Yamaguchi, Y.
• Funding Organization(s): MEXT

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• 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

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

• PubMed: 27015765 
• 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 (GlcNAcβ1-2Man) 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin domain family 4 member A	A, B, C, D	134	Homo sapiens	Mutation(s): 0  Gene Names: CLEC4A, CLECSF6, DCIR, LLIR, HDCGC13P
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMR7 (Homo sapiens) Explore Q9UMR7  Go to UniProtKB:  Q9UMR7
PHAROS:  Q9UMR7 GTEx:  ENSG00000111729

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• 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 ( Å )	Angle ( ˚ )
a = 102.489	α = 90
b = 105.832	β = 90
c = 65.387	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-05-11 
Deposition Author(s): Nagae, M., Yamaguchi, Y.

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Funding Organization	Location	Grant Number
MEXT	Japan	24770111
MEXT	Japan	15K18496

Revision History  

• 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