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 1.3 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
  • Primary Citation of Related Structures:  
    3VPP

  • 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 and processing of material from dead cells ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-type lectin domain family 9 member AA, B132Homo sapiensMutation(s): 1 
Gene Names: CLEC9A, UNQ9341/PRO34046
UniProt
Find proteins for Q6UXN8 (Homo sapiens)
Explore Q6UXN8 
Go to UniProtKB:  Q6UXN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6UXN8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-04-28
    Changes: Database references, Derived calculations, Source and taxonomy