1P1Z

X-RAY CRYSTAL STRUCTURE OF THE LECTIN-LIKE NATURAL KILLER CELL RECEPTOR LY-49C BOUND TO ITS MHC CLASS I LIGAND H-2Kb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.26 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.263 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Variable MHC class I engagement by Ly49 natural killer cell receptors demonstrated by the crystal structure of Ly49C bound to H-2K(b).

Dam, J.Guan, R.Natarajan, K.Dimasi, N.Chlewicki, L.K.Kranz, D.M.Schuck, P.Margulies, D.H.Mariuzza, R.A.

(2003) Nat Immunol 4: 1213-1222

  • DOI: https://doi.org/10.1038/ni1006
  • Primary Citation of Related Structures:  
    1P1Z, 1P4L

  • PubMed Abstract: 

    The Ly49 family of natural killer (NK) receptors regulates NK cell function by sensing major histocompatibility complex (MHC) class I. Ly49 receptors show complex patterns of MHC class I cross-reactivity and, in certain cases, peptide selectivity. To investigate whether specificity differences result from topological differences in MHC class I engagement, we determined the structure of the peptide-selective receptor Ly49C in complex with H-2K(b). The Ly49C homodimer binds two MHC class I molecules in symmetrical way, a mode distinct from that of Ly49A, which binds MHC class I asymmetrically. Ly49C does not directly contact the MHC-bound peptide. In addition, MHC crosslinking by Ly49C was demonstrated in solution. We propose a dynamic model for Ly49-MHC class I interactions involving conformational changes in the receptor, whereby variations in Ly49 dimerization mediate different MHC-binding modes.


  • Organizational Affiliation

    Center for Advanced Research in Biotechnology, W.M. Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, K-B alpha chain274Mus musculusMutation(s): 0 
Gene Names: H2-K
UniProt
Find proteins for P01901 (Mus musculus)
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Go to UniProtKB:  P01901
Entity Groups  
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UniProt GroupP01901
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Mus musculusMutation(s): 0 
Gene Names: B2M
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
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Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ovalbumin peptideC [auth P]8N/AMutation(s): 0 
UniProt
Find proteins for P01012 (Gallus gallus)
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UniProt GroupP01012
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
LY49-C antigen120Mus musculusMutation(s): 0 
Gene Names: KLRA3 OR LY49C OR LY-49C
UniProt
Find proteins for Q64329 (Mus musculus)
Explore Q64329 
Go to UniProtKB:  Q64329
Entity Groups  
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UniProt GroupQ64329
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.26 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.263 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.047α = 90
b = 149.047β = 90
c = 64.383γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance