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PDBsum entry 2cde
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protein Protein-protein interface(s) links
Cell receptor PDB id
2cde

 

 

 

 

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Contents
Protein chains
192 a.a. *
244 a.a. *
* Residue conservation analysis
PDB id:
2cde
Name: Cell receptor
Title: Structure and binding kinetics of three different human cd1d-alpha- galactosylceramide specific t cell receptors - inkt-tcr
Structure: Inkt-tcr. Chain: a, c, e. Engineered: yes. Other_details: human invariant natural killer t cell receptor valpha 24 and vbeta11. Inkt-tcr. Chain: b, d, f. Engineered: yes. Other_details: human invariant natural killer t cell receptor valpha
Source: Homo sapiens. Human. Organism_taxid: 9606. Cell: natural killer t cell. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
3.50Å     R-factor:   0.283     R-free:   0.350
Authors: S.D.Gadola,M.Koch,J.Marles-Wright,N.M.Lissin,D.Sheperd,G.Matulis, K.Harlos,P.M.Villiger,D.I.Stuart,B.K.Jakobsen,V.Cerundolo,E.Y.Jones
Key ref: S.D.Gadola et al. (2006). Structure and binding kinetics of three different human CD1d-alpha-galactosylceramide-specific T cell receptors. J Exp Med, 203, 699-710. PubMed id: 16520393
Date:
23-Jan-06     Release date:   07-Mar-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 192 a.a.
Protein chains
Pfam   ArchSchema ?
P01850  (TRBC1_HUMAN) -  T cell receptor beta constant 1 from Homo sapiens
Seq:
Struc: 		176 a.a.
244 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 

 
J Exp Med 203:699-710 (2006)
PubMed id: 16520393  
 
 
Structure and binding kinetics of three different human CD1d-alpha-galactosylceramide-specific T cell receptors.
S.D.Gadola, M.Koch, J.Marles-Wright, N.M.Lissin, D.Shepherd, G.Matulis, K.Harlos, P.M.Villiger, D.I.Stuart, B.K.Jakobsen, V.Cerundolo, E.Y.Jones.
 
  ABSTRACT  
 
Invariant human TCR Valpha24-Jalpha18+/Vbeta11+ NKT cells (iNKT) are restricted by CD1d-alpha-glycosylceramides. We analyzed crystal structures and binding characteristics for an iNKT TCR plus two CD1d-alpha-GalCer-specific Vbeta11+ TCRs that use different TCR Valpha chains. The results were similar to those previously reported for MHC-peptide-specific TCRs, illustrating the versatility of the TCR platform. Docking TCR and CD1d-alpha-GalCer structures provided plausible insights into their interaction. The model supports a diagonal orientation of TCR on CD1d and suggests that complementarity determining region (CDR)3alpha, CDR3beta, and CDR1beta interact with ligands presented by CD1d, whereas CDR2beta binds to the CD1d alpha1 helix. This docking provides an explanation for the dominant usage of Vbeta11 and Vbeta8.2 chains by human and mouse iNKT cells, respectively, for recognition of CD1d-alpha-GalCer.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23154222 J.Rossjohn, D.G.Pellicci, O.Patel, L.Gapin, and D.I.Godfrey (2012).
Recognition of CD1d-restricted antigens by natural killer T cells.
  Nat Rev Immunol, 12, 845-857.  
21298486 E.Champagne (2011).
γδ T cell Receptor Ligands and Modes of Antigen Recognition.
  Arch Immunol Ther Exp (Warsz), 59, 117-137.  
21376639 K.S.Wun, G.Cameron, O.Patel, S.S.Pang, D.G.Pellicci, L.C.Sullivan, S.Keshipeddy, M.H.Young, A.P.Uldrich, M.S.Thakur, S.K.Richardson, A.R.Howell, P.A.Illarionov, A.G.Brooks, G.S.Besra, J.McCluskey, L.Gapin, S.A.Porcelli, D.I.Godfrey, and J.Rossjohn (2011).
A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells.
  Immunity, 34, 327-339.
PDB codes: 3arb 3ard 3are 3arf 3arg
20072154 A.C.Chan, P.Neeson, E.Leeansyah, K.Tainton, H.Quach, H.M.Prince, D.I.Godfrey, D.Ritchie, and S.P.Berzins (2010).
Testing the NKT cell hypothesis in lenalidomide-treated myelodysplastic syndrome patients.
  Leukemia, 24, 592-600.  
19857519 G.De Libero, and L.Mori (2010).
How the immune system detects lipid antigens.
  Prog Lipid Res, 49, 120-127.  
20585371 G.Matulis, J.P.Sanderson, N.M.Lissin, M.B.Asparuhova, G.R.Bommineni, D.Schümperli, R.R.Schmidt, P.M.Villiger, B.K.Jakobsen, and S.D.Gadola (2010).
Innate-like control of human iNKT cell autoreactivity via the hypervariable CDR3beta loop.
  PLoS Biol, 8, e1000402.  
19594637 D.M.Zajonc, and M.Kronenberg (2009).
Carbohydrate specificity of the recognition of diverse glycolipids by natural killer T cells.
  Immunol Rev, 230, 188-200.  
  20948595 L.Teyton (2009).
Natural killer T cell recognition of lipid antigens.
  F1000 Biol Rep, 1, 0.  
19592274 T.Mallevaey, J.P.Scott-Browne, J.L.Matsuda, M.H.Young, D.G.Pellicci, O.Patel, M.Thakur, L.Kjer-Nielsen, S.K.Richardson, V.Cerundolo, A.R.Howell, J.McCluskey, D.I.Godfrey, J.Rossjohn, P.Marrack, and L.Gapin (2009).
T cell receptor CDR2 beta and CDR3 beta loops collaborate functionally to shape the iNKT cell repertoire.
  Immunity, 31, 60-71.  
19079136 V.Cerundolo, J.D.Silk, S.H.Masri, and M.Salio (2009).
Harnessing invariant NKT cells in vaccination strategies.
  Nat Rev Immunol, 9, 28-38.  
19816402 W.C.Florence, C.Xia, L.E.Gordy, W.Chen, Y.Zhang, J.Scott-Browne, Y.Kinjo, K.O.Yu, S.Keshipeddy, D.G.Pellicci, O.Patel, L.Kjer-Nielsen, J.McCluskey, D.I.Godfrey, J.Rossjohn, S.K.Richardson, S.A.Porcelli, A.R.Howell, K.Hayakawa, L.Gapin, D.M.Zajonc, P.G.Wang, and S.Joyce (2009).
Adaptability of the semi-invariant natural killer T-cell receptor towards structurally diverse CD1d-restricted ligands.
  EMBO J, 28, 3579-3590.  
19793337 Y.Ilan (2009).
Alpha versus beta: are we on the way to resolve the mystery as to which is the endogenous ligand for natural killer T cells?
  Clin Exp Immunol, 158, 300-307.  
18342005 D.I.Godfrey, J.Rossjohn, and J.McCluskey (2008).
The fidelity, occasional promiscuity, and versatility of T cell receptor recognition.
  Immunity, 28, 304-314.  
18295796 D.M.Zajonc, P.B.Savage, A.Bendelac, I.A.Wilson, and L.Teyton (2008).
Crystal structures of mouse CD1d-iGb3 complex and its cognate Valpha14 T cell receptor suggest a model for dual recognition of foreign and self glycolipids.
  J Mol Biol, 377, 1104-1116.
PDB codes: 2q7y 2q86
18253930 G.Denkberg, V.S.Stronge, E.Zahavi, P.Pittoni, R.Oren, D.Shepherd, M.Salio, C.McCarthy, P.A.Illarionov, A.van der Merwe, G.S.Besra, P.Dellabona, G.Casorati, V.Cerundolo, and Y.Reiter (2008).
Phage display-derived recombinant antibodies with TCR-like specificity against alpha-galactosylceramide and its analogues in complex with human CD1d molecules.
  Eur J Immunol, 38, 829-840.  
18593354 J.D.Silk, M.Salio, J.Brown, E.Y.Jones, and V.Cerundolo (2008).
Structural and functional aspects of lipid binding by CD1 molecules.
  Annu Rev Cell Dev Biol, 24, 369-395.  
18378792 K.S.Wun, N.A.Borg, L.Kjer-Nielsen, T.Beddoe, R.Koh, S.K.Richardson, M.Thakur, A.R.Howell, J.P.Scott-Browne, L.Gapin, D.I.Godfrey, J.McCluskey, and J.Rossjohn (2008).
A minimal binding footprint on CD1d-glycolipid is a basis for selection of the unique human NKT TCR.
  J Exp Med, 205, 939-949.  
18304006 P.Marrack, J.P.Scott-Browne, S.Dai, L.Gapin, and J.W.Kappler (2008).
Evolutionarily conserved amino acids that control TCR-MHC interaction.
  Annu Rev Immunol, 26, 171-203.  
17150027 A.Bendelac, P.B.Savage, and L.Teyton (2007).
The biology of NKT cells.
  Annu Rev Immunol, 25, 297-336.  
18022562 A.de Jong, E.C.Arce, T.Y.Cheng, R.P.van Summeren, B.L.Feringa, V.Dudkin, D.Crich, I.Matsunaga, A.J.Minnaard, and D.B.Moody (2007).
CD1c presentation of synthetic glycolipid antigens with foreign alkyl branching motifs.
  Chem Biol, 14, 1232-1242.  
17485514 C.McCarthy, D.Shepherd, S.Fleire, V.S.Stronge, M.Koch, P.A.Illarionov, G.Bossi, M.Salio, G.Denkberg, F.Reddington, A.Tarlton, B.G.Reddy, R.R.Schmidt, Y.Reiter, G.M.Griffiths, P.A.van der Merwe, G.S.Besra, E.Y.Jones, F.D.Batista, and V.Cerundolo (2007).
The length of lipids bound to human CD1d molecules modulates the affinity of NKT cell TCR and the threshold of NKT cell activation.
  J Exp Med, 204, 1131-1144.  
17581593 D.B.Moody (2007).
Immunology: how a T cell sees sugar.
  Nature, 448, 36-37.  
17951048 D.M.Zajonc, and M.Kronenberg (2007).
CD1 mediated T cell recognition of glycolipids.
  Curr Opin Struct Biol, 17, 521-529.  
17828267 J.P.Scott-Browne, J.L.Matsuda, T.Mallevaey, J.White, N.A.Borg, J.McCluskey, J.Rossjohn, J.Kappler, P.Marrack, and L.Gapin (2007).
Germline-encoded recognition of diverse glycolipids by natural killer T cells.
  Nat Immunol, 8, 1105-1113.  
18077358 M.Salio, A.O.Speak, D.Shepherd, P.Polzella, P.A.Illarionov, N.Veerapen, G.S.Besra, F.M.Platt, and V.Cerundolo (2007).
Modulation of human natural killer T cell ligands on TLR-mediated antigen-presenting cell activation.
  Proc Natl Acad Sci U S A, 104, 20490-20495.  
17581592 N.A.Borg, K.S.Wun, L.Kjer-Nielsen, M.C.Wilce, D.G.Pellicci, R.Koh, G.S.Besra, M.Bharadwaj, D.I.Godfrey, J.McCluskey, and J.Rossjohn (2007).
CD1d-lipid-antigen recognition by the semi-invariant NKT T-cell receptor.
  Nature, 448, 44-49.
PDB code: 2po6
18074396 R.L.Rich, and D.G.Myszka (2007).
Survey of the year 2006 commercial optical biosensor literature.
  J Mol Recognit, 20, 300-366.  
16855607 D.B.Moody (2006).
TLR gateways to CD1 function.
  Nat Immunol, 7, 811-817.  
16870416 E.Treiner, and O.Lantz (2006).
CD1d- and MR1-restricted invariant T cells: of mice and men.
  Curr Opin Immunol, 18, 519-526.  
17661645 G.Wingender, and M.Kronenberg (2006).
Invariant natural killer cells in the response to bacteria: the advent of specific antigens.
  Future Microbiol, 1, 325-340.  
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 codes are shown on the right.

 

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