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PDBsum entry 1kgc

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protein Protein-protein interface(s) links
Immune system PDB id
1kgc
Jmol
Contents
Protein chains
201 a.a. *
241 a.a. *
Waters ×686
* Residue conservation analysis
PDB id:
1kgc
Name: Immune system
Title: Immune receptor
Structure: T-cell receptor alpha chain. Chain: d. Engineered: yes. T-cell receptor beta chain. Chain: e. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.50Å     R-factor:   0.211     R-free:   0.234
Authors: L.Kjer-Nielsen,C.S.Clements,A.G.Brooks,A.W.Purcell, J.Mccluskey,J.Rossjohn
Key ref:
L.Kjer-Nielsen et al. (2002). The 1.5 A crystal structure of a highly selected antiviral T cell receptor provides evidence for a structural basis of immunodominance. Structure, 10, 1521-1532. PubMed id: 12429093 DOI: 10.1016/S0969-2126(02)00878-X
Date:
26-Nov-01     Release date:   11-Dec-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P01848  (TCA_HUMAN) -  T-cell receptor alpha chain C region
Seq:
Struc:
142 a.a.
201 a.a.
Protein chain
Pfam   ArchSchema ?
P01850  (TRBC1_HUMAN) -  T-cell receptor beta-1 chain C region
Seq:
Struc:
177 a.a.
241 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1016/S0969-2126(02)00878-X Structure 10:1521-1532 (2002)
PubMed id: 12429093  
 
 
The 1.5 A crystal structure of a highly selected antiviral T cell receptor provides evidence for a structural basis of immunodominance.
L.Kjer-Nielsen, C.S.Clements, A.G.Brooks, A.W.Purcell, J.McCluskey, J.Rossjohn.
 
  ABSTRACT  
 
Despite a potential repertoire of >10(15) alphabeta T cell receptors (TcR), the HLA B8-restricted cytolytic T cell response to a latent antigen of Epstein-Barr virus (EBV) is strikingly limited in the TcR sequences that are selected. Even in unrelated individuals this response is dominated by a single highly restricted TcR clonotype that selects identical combinations of hypervariable Valpha, Vbeta, D, J, and N region genes. We have determined the 1.5 A crystal structure of this "public" TcR, revealing that five of the six hypervariable loops adopt novel conformations providing a unique combining site that contains a deep pocket predicted to overlay the HLA B8-peptide complex. The findings suggest a structural basis for the immunodominance of this clonotype in the immune response to EBV.
 
  Selected figure(s)  
 
Figure 8.
Figure 8. Ball and Stick Stereo View Representation of the Public Sequences Selected in the LC13 TcR b Chain and the Residues with which They InteractThe CDR3b subdivided into three regions according to the origin of the relevant codons: Vb (red), Db and N (light blue), and Jb (green). The interacting residues are color-coded yellow (Vb) and gray (Va). Structural superposition of a region of the identical Jb segment from LC13 (green) and B7 (yellow) that highlights the conformational differences.
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 1521-1532) copyright 2002.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21301478 S.Gras, L.Kjer-Nielsen, Z.Chen, J.Rossjohn, and J.McCluskey (2011).
The structural bases of direct T-cell allorecognition: implications for T-cell-mediated transplant rejection.
  Immunol Cell Biol, 89, 388-395.  
21297580 Y.Yin, Y.Li, M.C.Kerzic, R.Martin, and R.A.Mariuzza (2011).
Structure of a TCR with high affinity for self-antigen reveals basis for escape from negative selection.
  EMBO J, 30, 1137-1148.
PDB code: 3o6f
21134635 M.E.Call, and J.J.Chou (2010).
A view into the blind spot: solution NMR provides new insights into signal transduction across the lipid bilayer.
  Structure, 18, 1559-1569.  
20944746 S.S.Pang, R.Berry, Z.Chen, L.Kjer-Nielsen, M.A.Perugini, G.F.King, C.Wang, S.H.Chew, N.L.La Gruta, N.K.Williams, T.Beddoe, T.Tiganis, N.P.Cowieson, D.I.Godfrey, A.W.Purcell, M.C.Wilce, J.McCluskey, and J.Rossjohn (2010).
The structural basis for autonomous dimerization of the pre-T-cell antigen receptor.
  Nature, 467, 844-848.
PDB code: 3of6
19139173 J.K.Archbold, W.A.Macdonald, S.Gras, L.K.Ely, J.J.Miles, M.J.Bell, R.M.Brennan, T.Beddoe, M.C.Wilce, C.S.Clements, A.W.Purcell, J.McCluskey, S.R.Burrows, and J.Rossjohn (2009).
Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition.
  J Exp Med, 206, 209-219.
PDB codes: 3dx6 3dx7 3dx8 3dx9 3dxa
19416894 K.Rubtsova, J.P.Scott-Browne, F.Crawford, S.Dai, P.Marrack, and J.W.Kappler (2009).
Many different Vbeta CDR3s can reveal the inherent MHC reactivity of germline-encoded TCR V regions.
  Proc Natl Acad Sci U S A, 106, 7951-7956.  
19464197 T.Beddoe, Z.Chen, C.S.Clements, L.K.Ely, S.R.Bushell, J.P.Vivian, L.Kjer-Nielsen, S.S.Pang, M.A.Dunstone, Y.C.Liu, W.A.Macdonald, M.A.Perugini, M.C.Wilce, S.R.Burrows, A.W.Purcell, T.Tiganis, S.P.Bottomley, J.McCluskey, and J.Rossjohn (2009).
Antigen ligation triggers a conformational change within the constant domain of the alphabeta T cell receptor.
  Immunity, 30, 777-788.  
20064448 W.A.Macdonald, Z.Chen, S.Gras, J.K.Archbold, F.E.Tynan, C.S.Clements, M.Bharadwaj, L.Kjer-Nielsen, P.M.Saunders, M.C.Wilce, F.Crawford, B.Stadinsky, D.Jackson, A.G.Brooks, A.W.Purcell, J.W.Kappler, S.R.Burrows, J.Rossjohn, and J.McCluskey (2009).
T cell allorecognition via molecular mimicry.
  Immunity, 31, 897-908.
PDB codes: 3kpl 3kpm 3kpn 3kpo 3kpp 3kpq 3kpr 3kps
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.  
18726714 E.J.Collins, and D.S.Riddle (2008).
TCR-MHC docking orientation: natural selection, or thymic selection?
  Immunol Res, 41, 267-294.  
18800968 K.M.Armstrong, K.H.Piepenbrink, and B.M.Baker (2008).
Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes.
  Biochem J, 415, 183-196.  
17259989 F.E.Tynan, H.H.Reid, L.Kjer-Nielsen, J.J.Miles, M.C.Wilce, L.Kostenko, N.A.Borg, N.A.Williamson, T.Beddoe, A.W.Purcell, S.R.Burrows, J.McCluskey, and J.Rossjohn (2007).
A T cell receptor flattens a bulged antigenic peptide presented by a major histocompatibility complex class I molecule.
  Nat Immunol, 8, 268-276.
PDB codes: 2nw2 2nw3 2nx5
17368054 M.S.Kuhns, and M.M.Davis (2007).
Disruption of extracellular interactions impairs T cell receptor-CD3 complex stability and signaling.
  Immunity, 26, 357-369.  
17011774 C.S.Clements, M.A.Dunstone, W.A.Macdonald, J.McCluskey, and J.Rossjohn (2006).
Specificity on a knife-edge: the alphabeta T cell receptor.
  Curr Opin Struct Biol, 16, 787-795.  
16963442 J.K.Archbold, W.A.Macdonald, J.J.Miles, R.M.Brennan, L.Kjer-Nielsen, J.McCluskey, S.R.Burrows, and J.Rossjohn (2006).
Alloreactivity between disparate cognate and allogeneic pMHC-I complexes is the result of highly focused, peptide-dependent structural mimicry.
  J Biol Chem, 281, 34324-34332.
PDB code: 2h6p
16505140 L.Kjer-Nielsen, N.A.Borg, D.G.Pellicci, T.Beddoe, L.Kostenko, C.S.Clements, N.A.Williamson, M.J.Smyth, G.S.Besra, H.H.Reid, M.Bharadwaj, D.I.Godfrey, J.Rossjohn, and J.McCluskey (2006).
A structural basis for selection and cross-species reactivity of the semi-invariant NKT cell receptor in CD1d/glycolipid recognition.
  J Exp Med, 203, 661-673.
PDB codes: 2eyr 2eys 2eyt
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.  
16473826 M.S.Kuhns, M.M.Davis, and K.C.Garcia (2006).
Deconstructing the form and function of the TCR/CD3 complex.
  Immunity, 24, 133-139.  
16260763 H.Li, S.Van Vranken, Y.Zhao, Z.Li, Y.Guo, L.Eisele, and Y.Li (2005).
Crystal structures of T cell receptor (beta) chains related to rheumatoid arthritis.
  Protein Sci, 14, 3025-3038.
PDB codes: 2axh 2axj
15609316 S.Oerke, H.Höhn, I.Zehbe, H.Pilch, K.H.Schicketanz, W.E.Hitzler, C.Neukirch, K.Freitag, and M.J.Maeurer (2005).
Naturally processed and HLA-B8-presented HPV16 E7 epitope recognized by T cells from patients with cervical cancer.
  Int J Cancer, 114, 766-778.  
15291817 A.G.Tzakos, P.Fuchs, N.A.van Nuland, A.Troganis, T.Tselios, S.Deraos, J.Matsoukas, I.P.Gerothanassis, and A.M.Bonvin (2004).
NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and its antagonist: structural implications for the MHC II (I-Au)-peptide complex from docking calculations.
  Eur J Biochem, 271, 3399-3413.  
15186260 J.E.Gumperz (2004).
Antigen specificity of semi-invariant CD1d-restricted T cell receptors: the best of both worlds?
  Immunol Cell Biol, 82, 285-294.  
12530971 A.J.Bankovich, and K.C.Garcia (2003).
Not just any T cell receptor will do.
  Immunity, 18, 7.  
12530975 L.Kjer-Nielsen, C.S.Clements, A.W.Purcell, A.G.Brooks, J.C.Whisstock, S.R.Burrows, J.McCluskey, and J.Rossjohn (2003).
A structural basis for the selection of dominant alphabeta T cell receptors in antiviral immunity.
  Immunity, 18, 53-64.
PDB code: 1mi5
12429085 E.J.Adams, and K.C.Garcia (2002).
A T cell receptor goes public.
  Structure, 10, 1468-1469.  
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.