PDBsum entry 1jsk

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Immune system PDB id
Jmol PyMol
Protein chains
123 a.a.* *
174 a.a.* *
* Residue conservation analysis
* C-alpha coords only
Superseded by: 4pp8
PDB id:
Name: Immune system
Title: Crystal structure of murine nk cell ligand rae-1 beta in com nkg2d
Structure: Nkg2-d. Chain: a, b. Fragment: receptor binding domain, residues 110-232. Synonym: mouse nk cell receptor nkg2d. Engineered: yes. Rae-1 beta. Chain: c. Fragment: receptor binding domain, residues 31-204. Synonym: retinoic acid early transcript beta.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: nkg2d. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rae-1 beta.
3.50Å     R-factor:   0.314     R-free:   0.330
Authors: P.Li,R.K.Strong
Key ref:
P.Li et al. (2002). Crystal structures of RAE-1beta and its complex with the activating immunoreceptor NKG2D. Immunity, 16, 77-86. PubMed id: 11825567 DOI: 10.1016/S1074-7613(02)00258-3
17-Aug-01     Release date:   20-Feb-02    

Protein chains
Pfam   ArchSchema ?
O54709  (NKG2D_MOUSE) -  NKG2-D type II integral membrane protein
232 a.a.
123 a.a.
Protein chain
Pfam   ArchSchema ?
O08603  (RAE1B_MOUSE) -  Retinoic acid early-inducible protein 1-beta
253 a.a.
174 a.a.
Key:    PfamA domain  Secondary structure


    Added reference    
DOI no: 10.1016/S1074-7613(02)00258-3 Immunity 16:77-86 (2002)
PubMed id: 11825567  
Crystal structures of RAE-1beta and its complex with the activating immunoreceptor NKG2D.
P.Li, G.McDermott, R.K.Strong.
Induced by retinoic acid and implicated in playing a role in development, rodent RAE-1 proteins are ligands for the activating immunoreceptor NKG2D, widely expressed on natural killer cells, T cells, and macrophages. RAE-1 proteins (alpha, beta, gamma, and delta) are distant major histocompatibility complex (MHC) class I homologs, comprising isolated alpha1alpha2 platform domains. The crystal structure of RAE-1beta was distorted from other MHC homologs and displayed noncanonical disulfide bonds. The loss of any remnant of a peptide binding groove was facilitated by the close approach of the groove-defining helices through a hydrophobic, leucine-rich interface. The RAE-1beta-murine NKG2D complex structure resembled the human NKG2D-MICA receptor-ligand complex and further demonstrated the promiscuity of the NKG2D ligand binding site.
  Selected figure(s)  
Figure 3.
Figure 3. Structures of Murine NKD NK Cell Receptor-Ligand ComplexesRibbon representations (top) and GRASP (Nicholls et al., 1991) molecular surfaces (bottom) are shown for the structures of (A) the muNKG2D–RAE-1β, (B) huNKG2D–MICA, and (C) Ly49A-H-2D^d complexes. Ribbons of the ligands are colored by domain: α1, yellow; α2, red; α3 (when present), green; and β[2]-m (when present), cyan; ribbons of the receptors are colored by chain: blue or purple. Molecular surfaces of the platform domains are oriented such that the view is looking down onto the NKG2D binding surface of RAE-1 and MICA. In (A), the molecular surface of muNKG2D was included in an orientation looking down onto the RAE-1 binding surface, as if the receptor had been peeled away from the complex. Molecular surfaces are colored by electrostatic potential, with positively charged areas in blue and negatively charged areas in red. In (C), the bound peptide in H-2D^d is shown in ball-and-stick representation.
Figure 4.
Figure 4. Interactions of RAE-1β-muNKG2D Complexes in the CrystalTwo views of the reciprocal, crystallographic interaction between muNKG2D homodimers are shown, a view perpendicular to a hypothetical cell-cell interface (top) and a view down onto the complexes (bottom). Molecules are shown as ribbon representations colored by domain (muNKG2D-A, blue; muNKG2D-B, purple; RAE-1β α1, yellow; and RAE-1β α2, orange). The approximate position of the crystallographic 6[1] screw axis is indicated, as are hypothetical cell surfaces and the paths of membrane anchor elements (black arrows). The position of Asn179 is indicated in red on the ribbons and by red arrows.
  The above figures are reprinted by permission from Cell Press: Immunity (2002, 16, 77-86) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21422170 Y.Li, Q.Wang, and R.A.Mariuzza (2011).
Structure of the human activating natural cytotoxicity receptor NKp30 bound to its tumor cell ligand B7-H6.
  J Exp Med, 208, 703-714.  
20032175 H.P.Su, K.Singh, A.G.Gittis, and D.N.Garboczi (2010).
The structure of the poxvirus A33 protein reveals a dimer of unique C-type lectin-like domains.
  J Virol, 84, 2502-2510.
PDB code: 3k7b
20166740 L.Zhi, J.Mans, M.J.Paskow, P.H.Brown, P.Schuck, S.Jonjić, K.Natarajan, and D.H.Margulies (2010).
Direct interaction of the mouse cytomegalovirus m152/gp40 immunoevasin with RAE-1 isoforms.
  Biochemistry, 49, 2443-2453.  
20976056 O.Cédile, N.Popa, F.Pollet-Villard, N.Garmy, e.l. .C.Ibrahim, and J.Boucraut (2010).
The NKG2D ligands RAE-1δ and RAE-1ε differ with respect to their receptor affinity, expression profiles and transcriptional regulation.
  PLoS One, 5, e13466.  
19688209 A.V.Romphruk, A.Romphruk, T.K.Naruse, S.Raroengjai, C.Puapairoj, H.Inoko, and C.Leelayuwat (2009).
Polymorphisms of NKG2D ligands: diverse RAET1/ULBP genes in northeastern Thais.
  Immunogenetics, 61, 611-617.  
19494006 J.Arapovic, T.Lenac, R.Antulov, B.Polic, Z.Ruzsics, L.N.Carayannopoulos, U.H.Koszinowski, A.Krmpotic, and S.Jonjic (2009).
Differential susceptibility of RAE-1 isoforms to mouse cytomegalovirus.
  J Virol, 83, 8198-8207.  
19011767 J.Mans, L.Zhi, M.J.Revilleza, L.Smith, A.Redwood, K.Natarajan, and D.H.Margulies (2009).
Structure and function of murine cytomegalovirus MHC-I-like molecules: how the virus turned the host defense to its advantage.
  Immunol Res, 43, 264-279.  
19424970 M.Wittenbrink, J.Spreu, and A.Steinle (2009).
Differential NKG2D binding to highly related human NKG2D ligands ULBP2 and RAET1G is determined by a single amino acid in the alpha2 domain.
  Eur J Immunol, 39, 1642-1651.  
18332182 E.J.Petrie, C.S.Clements, J.Lin, L.C.Sullivan, D.Johnson, T.Huyton, A.Heroux, H.L.Hoare, T.Beddoe, H.H.Reid, M.C.Wilce, A.G.Brooks, and J.Rossjohn (2008).
CD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence.
  J Exp Med, 205, 725-735.
PDB code: 3cdg
18809410 K.Y.Kwong, S.Baskar, H.Zhang, C.L.Mackall, and C.Rader (2008).
Generation, affinity maturation, and characterization of a human anti-human NKG2D monoclonal antibody with dual antagonistic and agonistic activity.
  J Mol Biol, 384, 1143-1156.  
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.  
17318646 J.M.Dijkstra, T.Katagiri, K.Hosomichi, K.Yanagiya, H.Inoko, M.Ototake, T.Aoki, K.Hashimoto, and T.Shiina (2007).
A third broad lineage of major histocompatibility complex (MHC) class I in teleost fish; MHC class II linkage and processed genes.
  Immunogenetics, 59, 305-321.  
17897947 J.Mans, K.Natarajan, A.Balbo, P.Schuck, D.Eikel, S.Hess, H.Robinson, H.Simic, S.Jonjic, C.T.Tiemessen, and D.H.Margulies (2007).
Cellular expression and crystal structure of the murine cytomegalovirus major histocompatibility complex class I-like glycoprotein, m153.
  J Biol Chem, 282, 35247-35258.
PDB code: 2o5n
18083576 L.C.Sullivan, C.S.Clements, T.Beddoe, D.Johnson, H.L.Hoare, J.Lin, T.Huyton, E.J.Hopkins, H.H.Reid, M.C.Wilce, J.Kabat, F.Borrego, J.E.Coligan, J.Rossjohn, and A.G.Brooks (2007).
The heterodimeric assembly of the CD94-NKG2 receptor family and implications for human leukocyte antigen-E recognition.
  Immunity, 27, 900-911.
PDB code: 3bdw
16352655 E.Duprat, M.P.Lefranc, and O.Gascuel (2006).
A simple method to predict protein-binding from aligned sequences--application to MHC superfamily and beta2-microglobulin.
  Bioinformatics, 22, 453-459.  
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.  
16551255 M.G.Rudolph, R.L.Stanfield, and I.A.Wilson (2006).
How TCRs bind MHCs, peptides, and coreceptors.
  Annu Rev Immunol, 24, 419-466.  
16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.
  FEBS J, 272, 6179-6217.  
15894612 D.Garrity, M.E.Call, J.Feng, and K.W.Wucherpfennig (2005).
The activating NKG2D receptor assembles in the membrane with two signaling dimers into a hexameric structure.
  Proc Natl Acad Sci U S A, 102, 7641-7646.  
15939022 I.Ohki, T.Ishigaki, T.Oyama, S.Matsunaga, Q.Xie, M.Ohnishi-Kameyama, T.Murata, D.Tsuchiya, S.Machida, K.Morikawa, and S.Tate (2005).
Crystal structure of human lectin-like, oxidized low-density lipoprotein receptor 1 ligand binding domain and its ligand recognition mode to OxLDL.
  Structure, 13, 905-917.
PDB codes: 1yxj 1yxk
15771571 L.L.Lanier (2005).
NK cell recognition.
  Annu Rev Immunol, 23, 225-274.  
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.  
16089503 R.Olson, K.E.Huey-Tubman, C.Dulac, and P.J.Bjorkman (2005).
Structure of a pheromone receptor-associated MHC molecule with an open and empty groove.
  PLoS Biol, 3, e257.
PDB code: 1zs8
15802267 S.Huang, S.Gilfillan, M.Cella, M.J.Miley, O.Lantz, L.Lybarger, D.H.Fremont, and T.H.Hansen (2005).
Evidence for MR1 antigen presentation to mucosal-associated invariant T cells.
  J Biol Chem, 280, 21183-21193.  
14670298 B.J.McFarland, and R.K.Strong (2003).
Thermodynamic analysis of degenerate recognition by the NKG2D immunoreceptor: not induced fit but rigid adaptation.
  Immunity, 19, 803-812.  
14670294 D.H.Margulies (2003).
Molecular interactions: stiff or floppy (or somewhere in between?).
  Immunity, 19, 772-774.  
14523385 D.H.Raulet (2003).
Roles of the NKG2D immunoreceptor and its ligands.
  Nat Rev Immunol, 3, 781-790.  
12547506 G.Das, and C.A.Janeway (2003).
MHC specificity of iIELs.
  Trends Immunol, 24, 88-93.  
12787763 J.Jameson, D.Witherden, and W.L.Havran (2003).
T-cell effector mechanisms: gammadelta and CD1d-restricted subsets.
  Curr Opin Immunol, 15, 349-353.  
14563312 M.Gleimer, and P.Parham (2003).
Stress management: MHC class I and class I-like molecules as reporters of cellular stress.
  Immunity, 19, 469-477.  
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.  
11973127 E.Vivier, E.Tomasello, and P.Paul (2002).
Lymphocyte activation via NKG2D: towards a new paradigm in immune recognition?
  Curr Opin Immunol, 14, 306-311.  
12183162 K.L.McQueen, and P.Parham (2002).
Variable receptors controlling activation and inhibition of NK cells.
  Curr Opin Immunol, 14, 615-621.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.