3JQH

Structure of the neck region of the glycan-binding receptor DC-SIGNR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.201 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Segmented helical structure of the neck region of the glycan-binding receptor DC-SIGNR.

Feinberg, H.Tso, C.K.Taylor, M.E.Drickamer, K.Weis, W.I.

(2009) J.Mol.Biol. 394: 613-620

  • DOI: 10.1016/j.jmb.2009.10.006

  • PubMed Abstract: 
  • Carbohydrate-recognition domains (CRDs) in the glycan-binding receptors DC-SIGN (dendritic-cell-specific intercellular adhesion molecule 1-grabbing nonintegrin; CD209) and DC-SIGNR (DC-SIGN-related receptor, also known as L-SIGN and variously designa ...

    Carbohydrate-recognition domains (CRDs) in the glycan-binding receptors DC-SIGN (dendritic-cell-specific intercellular adhesion molecule 1-grabbing nonintegrin; CD209) and DC-SIGNR (DC-SIGN-related receptor, also known as L-SIGN and variously designated CD209L and CD299) are projected from the membrane surface by extended neck domains containing multiple repeats of a largely conserved 23-amino-acid sequence motif. Crystals of a fragment of the neck domain of DC-SIGNR containing multiple repeats in which each molecule extends through multiple unit cells, such that the observed crystallographic asymmetric unit represents one repeat averaged over six repeats of the protein, have been obtained. The repeats are largely alpha-helical. Based on the structure and arrangement of the repeats in the crystal, the neck region can be described as a series of four-helix bundles connected by short, non-helical linkers. Combining the structure of the isolated neck domain with a previously determined overlapping structure of the distal end of the neck region with the CRDs attached provides a model of the almost-complete extracellular portion of the receptor. The results are consistent with previous characterization of the extended structure for the isolated neck region and the extracellular domain. The organization of the neck suggests how CRDs may be disposed differently in DC-SIGN compared with DC-SIGNR and in variant forms of DC-SIGNR assembled from polypeptides with different numbers of repeats in the neck domain.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-type lectin domain family 4 member M
A
167Homo sapiensMutation(s): 0 
Gene Names: CLEC4M (CD209L, CD209L1, CD299)
Find proteins for Q9H2X3 (Homo sapiens)
Go to Gene View: CLEC4M
Go to UniProtKB:  Q9H2X3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.201 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 34.170α = 90.00
b = 34.170β = 90.00
c = 36.720γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
PHENIXphasing
SCALAdata scaling
Blu-Icedata collection
PHENIXrefinement
PHENIXmodel building
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description