PDBsum entry 1ja3

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protein Protein-protein interface(s) links
Immune system PDB id
Protein chains
115 a.a. *
113 a.a. *
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Crystal structure of the murine nk cell inhibitory receptor ly-49i
Structure: Mhc class i recognition receptor ly49i. Chain: a, b. Fragment: c-type lectin-like domain. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Strain: 129-j. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
3.00Å     R-factor:   0.333     R-free:   0.308
Authors: N.Dimasi,W.M.Sawicki,L.A.Reineck,Y.Li,K.Natarajan, D.H.Murgulies,A.R.Mariuzza
Key ref:
N.Dimasi et al. (2002). Crystal structure of the Ly49I natural killer cell receptor reveals variability in dimerization mode within the Ly49 family. J Mol Biol, 320, 573-585. PubMed id: 12096910 DOI: 10.1016/S0022-2836(02)00498-9
29-May-01     Release date:   17-Jul-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9JHN9  (Q9JHN9_MOUSE) -  MHC class I recognition receptor Ly49I
266 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
Q9JHN9  (Q9JHN9_MOUSE) -  MHC class I recognition receptor Ly49I
266 a.a.
113 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     carbohydrate binding     1 term  


DOI no: 10.1016/S0022-2836(02)00498-9 J Mol Biol 320:573-585 (2002)
PubMed id: 12096910  
Crystal structure of the Ly49I natural killer cell receptor reveals variability in dimerization mode within the Ly49 family.
N.Dimasi, M.W.Sawicki, L.A.Reineck, Y.Li, K.Natarajan, D.H.Margulies, R.A.Mariuzza.
Natural killer (NK) cells play a crucial role in the detection and destruction of virally infected and tumor cells during innate immune responses. The cytolytic activity of NK cells is regulated through a balance of inhibitory and stimulatory signals delivered by NK receptors that recognize classical major histocompatabilty complex class I (MHC-I) molecules, or MHC-I homologs such as MICA, on target cells. The Ly49 family of NK receptors (Ly49A through W), which includes both inhibitory and activating receptors, are homodimeric type II transmembrane glycoproteins, with each subunit composed of a C-type lectin-like domain tethered to the membrane by a stalk region. We have determined the crystal structure, at 3.0 A resolution, of the murine inhibitory NK receptor Ly49I. The Ly49I monomer adopts a fold similar to that of other C-type lectin-like NK receptors, including Ly49A, NKG2D and CD69. However, the Ly49I monomers associate in a manner distinct from that of these other NK receptors, forming a more open dimer. As a result, the putative MHC-binding surfaces of the Ly49I dimer are spatially more distant than the corresponding surfaces of Ly49A or NKG2D. These structural differences probably reflect the fundamentally different ways in which Ly49 and NKG2D receptors recognize their respective ligands: whereas the single MICA binding site of NKG2D is formed by the precise juxtaposition of two monomers, each Ly49 monomer contains an independent binding site for MHC-I. Hence, the structural constraints on dimerization geometry may be relatively relaxed within the Ly49 family. Such variability may enable certain Ly49 receptors, like Ly49I, to bind MHC-I molecules bivalently, thereby stabilizing receptor-ligand interactions and enhancing signal transmission to the NK cell.
  Selected figure(s)  
Figure 3.
Figure 3. Superposition of the putative MHC-binding region of Ly49I onto the ligand-binding sites of Ly49A, NKG2D and MBP-A. Loops and b-strands are labeled according to Figure 2. The inset shows hot-spot residues Ser236, Arg239 and Asp241 of Ly49A [15.] superposed on the corresponding residues of Ly49I.
Figure 5.
Figure 5. Ball-and-stick representations of NKD dimer interfaces. (a) The b0 interfaces of the Ly49I, Ly49A,[16.] CD69 [22.] and NKG2D [24.] homodimers. Hydrogen bonds linking the anti-parallel b-strands are drawn as black dotted lines. All residues are labeled. Carbon atoms are light blue, nitrogen atoms are dark blue, oxygen atoms are red, and sulfur atoms are yellow. (b) Comparison of the b0 interface of Ly49I with those of Ly49A, NKG2D and CD69. If one monomer of the Ly49A dimer is aligned through the a-carbon atoms of residues 142-146 of strand b0 with one monomer of the Ly49I dimer, strand b0 of the other Ly49A monomer is rotated 63° and translated 14 Å with respect to the corresponding b0 strand of Ly49I. Similar results are observed in comparisons of Ly49I with NKG2D and CD69.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 573-585) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18948016 M.Pyzik, A.Kielczewska, and S.M.Vidal (2008).
NK cell receptors and their MHC class I ligands in host response to cytomegalovirus: insights from the mouse genome.
  Semin Immunol, 20, 331-342.  
18574582 S.L.Rogers, and J.Kaufman (2008).
High allelic polymorphism, moderate sequence diversity and diversifying selection for B-NK but not B-lec, the pair of lectin-like receptor genes in the chicken MHC.
  Immunogenetics, 60, 461-475.  
16737824 L.Deng, and R.A.Mariuzza (2006).
Structural basis for recognition of MHC and MHC-like ligands by natural killer cell receptors.
  Semin Immunol, 18, 159-166.  
16737823 S.Malarkannan (2006).
The balancing act: inhibitory Ly49 regulate NKG2D-mediated NK cell functions.
  Semin Immunol, 18, 186-192.  
16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.
  FEBS J, 272, 6179-6217.  
15661035 N.Dimasi, and R.Biassoni (2005).
Structural and functional aspects of the Ly49 natural killer cell receptors.
  Immunol Cell Biol, 83, 1-8.  
20476991 R.Biassoni, and N.Dimasi (2005).
Human natural killer cell receptor functions and their implication in diseases.
  Expert Rev Clin Immunol, 1, 405-417.  
14732928 R.L.Rich, and D.G.Myszka (2003).
A survey of the year 2002 commercial optical biosensor literature.
  J Mol Recognit, 16, 351-382.  
12471063 S.Radaev, and P.D.Sun (2003).
Structure and function of natural killer cell surface receptors.
  Annu Rev Biophys Biomol Struct, 32, 93.  
12669021 W.M.Yokoyama, and B.F.Plougastel (2003).
Immune functions encoded by the natural killer gene complex.
  Nat Rev Immunol, 3, 304-316.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.