3WBQ

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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 --: --

  • DOI: 10.1002/prot.24504
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
C-type lectin domain family 4 member C
A, B
130Homo sapiensMutation(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 = 117.185α = 90.00
b = 37.324β = 116.93
c = 70.957γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SERGUIdata collection
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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