3VPP

Crystal Structure of the Human CLEC9A C-type Lectin-Like Domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The dendritic cell receptor Clec9A binds damaged cells via exposed actin filaments.

Zhang, J.G., Czabotar, P.E., Policheni, A.N., Caminschi, I., Wan, S.S., Kitsoulis, S., Tullett, K.M., Robin, A.Y., Brammananth, R., van Delft, M.F., Lu, J., O'Reilly, L.A., Josefsson, E.C., Kile, B.T., Chin, W.J., Mintern, J.D., Olshina, M.A., Wong, W., Baum, J., Wright, M.D., Huang, D.C., Mohandas, N., Coppel, R.L., Colman, P.M., Nicola, N.A., Shortman, K., Lahoud, M.H.

(2012) Immunity 36: 646-657

  • DOI: 10.1016/j.immuni.2012.03.009
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • The immune system must distinguish viable cells from cells damaged by physical and infective processes. The damaged cell-recognition molecule Clec9A is expressed on the surface of the mouse and human dendritic cell subsets specialized for the uptake ...

    The immune system must distinguish viable cells from cells damaged by physical and infective processes. The damaged cell-recognition molecule Clec9A is expressed on the surface of the mouse and human dendritic cell subsets specialized for the uptake and processing of material from dead cells. Clec9A recognizes a conserved component within nucleated and nonnucleated cells, exposed when cell membranes are damaged. We have identified this Clec9A ligand as a filamentous form of actin in association with particular actin-binding domains of cytoskeletal proteins. We have determined the crystal structure of the human CLEC9A C-type lectin domain and propose a functional dimeric structure with conserved tryptophans in the ligand recognition site. Mutation of these residues ablated CLEC9A binding to damaged cells and to the isolated ligand complexes. We propose that Clec9A provides targeted recruitment of the adaptive immune system during infection and can also be utilized to enhance immune responses generated by vaccines.

    Organizational Affiliation: 

    The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-type lectin domain family 9 member A
A, B
132Homo sapiensMutation(s): 1 
Gene Names: CLEC9A, UNQ9341/PRO34046
Find proteins for Q6UXN8 (Homo sapiens)
Go to UniProtKB:  Q6UXN8
NIH Common Fund Data Resources
PHAROS  Q6UXN8
GTEx  ENSG00000197992
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.17α = 90
b = 53.824β = 109.35
c = 57.446γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Database references
  • Version 1.2: 2014-04-16
    Changes: Experimental preparation