Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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: 30.26 kDa 
• Atom Count: 2055 
• Modelled Residue Count: 250 
• Deposited 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)

• PDB DOI: 10.2210/pdb3WBQ/pdb

• Classification: Carbohydrate Binding Protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.30 Å
• R-Value Free: 0.293 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 

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:  
  3WBP, 3WBQ, 3WBR


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin domain family 4 member C	A, B	130	Homo sapiens	Mutation(s): 0  Gene Names: BDCA2, CLEC4C, CLECSF11, CLECSF7, DLEC, HECL, UNQ9361/PRO34150
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTT0 (Homo sapiens) Explore Q8WTT0  Go to UniProtKB:  Q8WTT0
PHAROS:  Q8WTT0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.293 
• R-Value Work: 0.236 
• R-Value Observed: 0.239 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.185	α = 90
b = 37.324	β = 116.93
c = 70.957	γ = 90

Software Package:

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

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
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description