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PDBsum entry 1mpu

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protein ligands links
Immune system PDB id
1mpu
Jmol
Contents
Protein chain
128 a.a. *
Ligands
PO4
Waters ×105
* Residue conservation analysis
PDB id:
1mpu
Name: Immune system
Title: Crystal structure of the free human nkg2d immunoreceptor
Structure: Nkg2-d type ii integral membrane protein. Chain: a. Fragment: residues 80-216. Synonym: nkg2-d activating nk receptor, nk cell receptor d. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
2.50Å     R-factor:   0.245     R-free:   0.296
Authors: B.J.Mcfarland,T.Kortemme,D.Baker,R.K.Strong
Key ref:
B.J.McFarland et al. (2003). Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands. Structure, 11, 411-422. PubMed id: 12679019 DOI: 10.1016/S0969-2126(03)00047-9
Date:
12-Sep-02     Release date:   15-Apr-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P26718  (NKG2D_HUMAN) -  NKG2-D type II integral membrane protein
Seq:
Struc:
216 a.a.
128 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/S0969-2126(03)00047-9 Structure 11:411-422 (2003)
PubMed id: 12679019  
 
 
Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands.
B.J.McFarland, T.Kortemme, S.F.Yu, D.Baker, R.K.Strong.
 
  ABSTRACT  
 
Engagement of diverse protein ligands (MIC-A/B, ULBP, Rae-1, or H60) by NKG2D immunoreceptors mediates elimination of tumorigenic or virally infected cells by natural killer and T cells. Three previous NKG2D-ligand complex structures show the homodimeric receptor interacting with the monomeric ligands in similar 2:1 complexes, with an equivalent surface on each NKG2D monomer binding intimately to a total of six distinct ligand surfaces. Here, the crystal structure of free human NKG2D and in silico and in vitro alanine-scanning mutagenesis analyses of the complex interfaces indicate that NKG2D recognition degeneracy is not explained by a classical induced-fit mechanism. Rather, the divergent ligands appear to utilize different strategies to interact with structurally conserved elements of the consensus NKG2D binding site.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Tabulation of NKG2D-Ligand ContactsResidue-residue contacts have been tabulated from the original structure references [12, 13 and 16], with ligand residues colored by the type of interaction observed as in Figure 2. Receptor murine/human sequence differences are colored red.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 411-422) copyright 2003.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20462859 F.Lauck, C.A.Smith, G.F.Friedland, E.L.Humphris, and T.Kortemme (2010).
RosettaBackrub--a web server for flexible backbone protein structure modeling and design.
  Nucleic Acids Res, 38, W569-W575.  
20653426 H.Huang, X.Zheng, Z.Tian, and R.Sun (2010).
Peptide mimicry of AICL inhibits cytolysis of NK cells by blocking NKp80-AICL recognition.
  Immunol Invest, 39, 587-597.  
  20536569 M.Champsaur, and L.L.Lanier (2010).
Effect of NKG2D ligand expression on host immune responses.
  Immunol Rev, 235, 267-285.  
20090832 S.Müller, G.Zocher, A.Steinle, and T.Stehle (2010).
Structure of the HCMV UL16-MICB complex elucidates select binding of a viral immunoevasin to diverse NKG2D ligands.
  PLoS Pathog, 6, e1000723.
PDB code: 2wy3
19414815 J.E.Butler, M.B.Moore, S.R.Presnell, H.W.Chan, N.J.Chalupny, and C.T.Lutz (2009).
Proteasome regulation of ULBP1 transcription.
  J Immunol, 182, 6600-6609.  
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.  
19631280 P.Obeidy, and A.F.Sharland (2009).
NKG2D and its ligands.
  Int J Biochem Cell Biol, 41, 2364-2367.  
18155234 C.McBeth, A.Seamons, J.C.Pizarro, S.J.Fleishman, D.Baker, T.Kortemme, J.M.Goverman, and R.K.Strong (2008).
A new twist in TCR diversity revealed by a forbidden alphabeta TCR.
  J Mol Biol, 375, 1306-1319.
PDB codes: 2p1y 2p24
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
  18832705 S.C.Wesselkamper, B.L.Eppert, G.T.Motz, G.W.Lau, D.J.Hassett, and M.T.Borchers (2008).
NKG2D is critical for NK cell activation in host defense against Pseudomonas aeruginosa respiratory infection.
  J Immunol, 181, 5481-5489.  
18193361 S.J.Burgess, K.Maasho, M.Masilamani, S.Narayanan, F.Borrego, and J.E.Coligan (2008).
The NKG2D receptor: immunobiology and clinical implications.
  Immunol Res, 40, 18-34.  
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.  
17132623 A.A.Watson, J.Brown, K.Harlos, J.A.Eble, T.S.Walter, and C.A.O'Callaghan (2007).
The crystal structure and mutational binding analysis of the extracellular domain of the platelet-activating receptor CLEC-2.
  J Biol Chem, 282, 3165-3172.
PDB code: 2c6u
17690100 C.S.Lengyel, L.J.Willis, P.Mann, D.Baker, T.Kortemme, R.K.Strong, and B.J.McFarland (2007).
Mutations designed to destabilize the receptor-bound conformation increase MICA-NKG2D association rate and affinity.
  J Biol Chem, 282, 30658-30666.  
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
17041605 E.S.Huseby, F.Crawford, J.White, P.Marrack, and J.W.Kappler (2006).
Interface-disrupting amino acids establish specificity between T cell receptors and complexes of major histocompatibility complex and peptide.
  Nat Immunol, 7, 1191-1199.  
16914326 J.D.Coudert, and W.Held (2006).
The role of the NKG2D receptor for tumor immunity.
  Semin Cancer Biol, 16, 333-343.  
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.  
16618592 R.A.Mariuzza (2006).
Multiple paths to multispecificity.
  Immunity, 24, 359-361.
PDB codes: 2a6d 2a6i 2a6j 2a6k
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
15549676 R.L.Rich, and D.G.Myszka (2005).
Survey of the year 2003 commercial optical biosensor literature.
  J Mol Recognit, 18, 1.  
14734107 L.N.Carayannopoulos, and W.M.Yokoyama (2004).
Recognition of infected cells by natural killer cells.
  Curr Opin Immunol, 16, 26-33.  
15193311 R.B.Russell, F.Alber, P.Aloy, F.P.Davis, D.Korkin, M.Pichaud, M.Topf, and A.Sali (2004).
A structural perspective on protein-protein interactions.
  Curr Opin Struct Biol, 14, 313-324.  
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.  
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.  
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.