Biological Assembly 1  

 3D View: Structure | Electron Density

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 30255.74 
• Atom Count: 2051 
• Residue Count: 260 
• Unique protein chains: 1

3WBQ

Crystal structure of carbohydrate recognition domain of Blood Dendritic Cell Antigen-2 (BDCA2) lectin (crystal form-2)

• DOI: 10.2210/pdb3WBQ/pdb

• Classification: Carbohydrate Binding Protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2013-05-20 Released: 2013-12-25 
• Deposition Author(s): Nagae, M., Ikeda, A., Kitago, Y., Matsumoto, N., Yamamoto, K., Yamaguchi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.293 
• R-Value Work: 0.236 

Literature

Crystal structures of carbohydrate recognition domain of blood dendritic cell antigen-2 (BDCA2) reveal a common domain-swapped dimer

Nagae, M., Ikeda, A., Kitago, Y., Matsumoto, N., Yamamoto, K., Yamaguchi, Y.

(2013) Proteins --: --

• PubMed: 24425442 
• DOI: 10.1002/prot.24504
• Primary Citation of Related Structures:  
  3WBR, 3WBP


• PubMed Abstract: 
  

We report on crystal structures of a carbohydrate recognition domain (CRD) of human C-type lectin receptor blood dendritic cell antigen-2 (BDCA2). Three different crystal forms were obtained at 1.8-2.3 Å resolution. In all three, the CRD has a basic C-type lectin fold, but a long loop extends away from the core domain to form a domain-swapped dimer. The structures of the dimers from the three different crystal forms superimpose well, indicating that domain swapping and dimer formation are energetically stable. The structure of the dimer is compared with other domain-swapped proteins, and a possible regulation mechanism of BDCA2 is discussed.

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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, 351-0198, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
C-type lectin domain family 4 member C	A, B	130	Homo sapiens	Mutation(s): 0  Gene Names: CLEC4C (BDCA2, CLECSF11, CLECSF7, DLEC, HECL)
Find proteins for Q8WTT0 (Homo sapiens) Go to Gene View: CLEC4C Go to UniProtKB:  Q8WTT0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.293 
• R-Value Work: 0.236 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 117.185	α = 90.00
b = 37.324	β = 116.93
c = 70.957	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
SERGUI	data collection
MOLREP	phasing
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-20 
• Released Date: 2013-12-25 
• Deposition Author(s): Nagae, M., Ikeda, A., Kitago, Y., Matsumoto, N., Yamamoto, K., Yamaguchi, Y.

Revision History 

• Version 1.0: 2013-12-25
  Type: Initial release
• Version 1.1: 2014-04-09
  Type: Database references
• Version 1.2: 2017-11-22
  Type: Refinement description