3C8K

The crystal structure of Ly49C bound to H-2Kb

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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


Literature

Molecular architecture of the major histocompatibility complex class I-binding site of Ly49 natural killer cell receptors.

Deng, L., Cho, S., Malchiodi, E.L., Kerzic, M.C., Dam, J., Mariuzza, R.A.

(2008) J Biol Chem 283: 16840-16849

  • DOI: 10.1074/jbc.M801526200
  • Primary Citation of Related Structures:  
    3C8J, 3C8K, 3CAD

  • PubMed Abstract: 

    • Natural killer (NK) cells play a vital role in the detection and destruction of virally infected and tumor cells during innate immune responses. The highly polymorphic Ly49 family of NK receptors regulates NK cell function by sensing major histocompatibility complex class I (MHC-I) molecules on target cells ...

    Natural killer (NK) cells play a vital role in the detection and destruction of virally infected and tumor cells during innate immune responses. The highly polymorphic Ly49 family of NK receptors regulates NK cell function by sensing major histocompatibility complex class I (MHC-I) molecules on target cells. Despite the determination of two Ly49-MHC-I complex structures, the molecular features of Ly49 receptors that confer specificity for particular MHC-I alleles have not been identified. To understand the functional architecture of Ly49-binding sites, we determined the crystal structures of Ly49C and Ly49G and completed refinement of the Ly49C-H-2K(b) complex. This information, combined with mutational analysis of Ly49A, permitted a structure-based classification of Ly49s that we used to dissect the binding site into three distinct regions, each having different roles in MHC recognition. One region, located at the center of the binding site, has a similar structure across the Ly49 family and mediates conserved interactions with MHC-I that contribute most to binding. However, the preference of individual Ly49s for particular MHC-I molecules is governed by two regions that flank the central region and are structurally more variable. One of the flanking regions divides Ly49s into those that recognize both H-2D and H-2K versus only H-2D ligands, whereas the other discriminates among H-2D or H-2K alleles. The modular design of Ly49-binding sites provides a framework for predicting the MHC-binding specificity of Ly49s that have not been characterized experimentally.

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, K-B alpha chainA274Mus musculusMutation(s): 0 
Gene Names: H2-K1, H2-K
UniProt
Find proteins for P01901 (Mus musculus)
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Go to UniProtKB:  P01901
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UniProt GroupP01901
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
beta-2 microglobulinB99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
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IMPC:  MGI:88127
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UniProt GroupP01887
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Entity ID: 3
MoleculeChainsSequence 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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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Natural killer cell receptor Ly-49CD125Mus musculusMutation(s): 3 
Gene Names: Klra3, Ly-49c, Ly49C
UniProt
Find proteins for Q64329 (Mus musculus)
Explore Q64329 
Go to UniProtKB:  Q64329
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UniProt GroupQ64329
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.01α = 90
b = 152.01β = 90
c = 64.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references