PDBsum entry 3c6l

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protein metals Protein-protein interface(s) links
Sugar binding protein/immune system PDB id
Protein chains
185 a.a. *
227 a.a. *
182 a.a. *
192 a.a. *
_CA ×3
* Residue conservation analysis
PDB id:
Name: Sugar binding protein/immune system
Title: Crystal structure of mouse mhc class ii i-ab/3k peptide complexed with mouse tcr 2w20
Structure: Tcr 2w20 alpha chain. Chain: a, e. Engineered: yes. Tcr 2w20 beta chain. Chain: b, f. Engineered: yes. H-2 class ii histocompatibility antigen, a-b alpha chain. Chain: c, g.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: h2-aa. Gene: h2-ab1, h2-iabeta.
3.40Å     R-factor:   0.268     R-free:   0.325
Authors: S.Dai
Key ref: S.Dai et al. (2008). Crossreactive T Cells spotlight the germline rules for alphabeta T cell-receptor interactions with MHC molecules. Immunity, 28, 324-334. PubMed id: 18308592
04-Feb-08     Release date:   29-Apr-08    
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Protein chains
No UniProt id for this chain
Struc: 185 a.a.
Protein chains
No UniProt id for this chain
Struc: 227 a.a.
Protein chains
Pfam   ArchSchema ?
P14434  (HA2B_MOUSE) -  H-2 class II histocompatibility antigen, A-B alpha chain
256 a.a.
182 a.a.
Protein chains
Pfam   ArchSchema ?
P14483  (HB2A_MOUSE) -  H-2 class II histocompatibility antigen, A beta chain
265 a.a.
192 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 13 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   2 terms 
  Biological process     immune response   2 terms 


Immunity 28:324-334 (2008)
PubMed id: 18308592  
Crossreactive T Cells spotlight the germline rules for alphabeta T cell-receptor interactions with MHC molecules.
S.Dai, E.S.Huseby, K.Rubtsova, J.Scott-Browne, F.Crawford, W.A.Macdonald, P.Marrack, J.W.Kappler.
To test whether highly crossreactive alphabeta T cell receptors (TCRs) produced during limited negative selection best illustrate evolutionarily conserved interactions between TCR and major histocompatibility complex (MHC) molecules, we solved the structures of three TCRs bound to the same MHC II peptide (IAb-3K). The TCRs had similar affinities for IAb-3K but varied from noncrossreactive to extremely crossreactive with other peptides and MHCs. Crossreactivity correlated with a shrinking, increasingly hydrophobic TCR-ligand interface, involving fewer TCR amino acids. A few CDR1 and CDR2 amino acids dominated the most crossreactive TCR interface with MHC, including Vbeta8 48Y and 54E and Valpha4 29Y, arranged to impose the familiar diagonal orientation of TCR on MHC. These interactions contribute to MHC binding by other TCRs using related V regions, but not usually so dominantly. These data show that crossreactive TCRs can spotlight the evolutionarily conserved features of TCR-MHC interactions and that these interactions impose the diagonal docking of TCRs on MHC.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21199956 D.K.Sethi, D.A.Schubert, A.K.Anders, A.Heroux, D.A.Bonsor, C.P.Thomas, E.J.Sundberg, J.Pyrdol, and K.W.Wucherpfennig (2011).
A highly tilted binding mode by a self-reactive T cell receptor results in altered engagement of peptide and MHC.
  J Exp Med, 208, 91.
PDB code: 3pl6
21321209 G.P.Morris, P.P.Ni, and P.M.Allen (2011).
Alloreactivity is limited by the endogenous peptide repertoire.
  Proc Natl Acad Sci U S A, 108, 3695-3700.  
21306912 K.W.Wucherpfennig, and D.Sethi (2011).
T cell receptor recognition of self and foreign antigens in the induction of autoimmunity.
  Semin Immunol, 23, 84-91.  
20931295 M.Cohn (2011).
On the logic of restrictive recognition of peptide by the T-cell antigen receptor.
  Immunol Res, 50, 49-68.  
  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.  
21173256 H.N.Eisen, and A.K.Chakraborty (2010).
Evolving concepts of specificity in immune reactions.
  Proc Natl Acad Sci U S A, 107, 22373-22380.  
20164930 J.B.Huppa, M.Axmann, M.A.Mörtelmaier, B.F.Lillemeier, E.W.Newell, M.Brameshuber, L.O.Klein, G.J.Schütz, and M.M.Davis (2010).
TCR-peptide-MHC interactions in situ show accelerated kinetics and increased affinity.
  Nature, 463, 963-967.  
20128915 K.S.Gunnarsen, E.Lunde, P.E.Kristiansen, B.Bogen, I.Sandlie, and G.A.Løset (2010).
Periplasmic expression of soluble single chain T cell receptors is rescued by the chaperone FkpA.
  BMC Biotechnol, 10, 8.  
  20452950 K.W.Wucherpfennig, E.Gagnon, M.J.Call, E.S.Huseby, and M.E.Call (2010).
Structural biology of the T-cell receptor: insights into receptor assembly, ligand recognition, and initiation of signaling.
  Cold Spring Harb Perspect Biol, 2, a005140.  
20333301 M.A.Patarroyo, A.Bermúdez, C.López, G.Yepes, and M.E.Patarroyo (2010).
3D analysis of the TCR/pMHCII complex formation in monkeys vaccinated with the first peptide inducing sterilizing immunity against human malaria.
  PLoS One, 5, e9771.  
20307209 M.K.Jenkins, H.H.Chu, J.B.McLachlan, and J.J.Moon (2010).
On the composition of the preimmune repertoire of T cells specific for Peptide-major histocompatibility complex ligands.
  Annu Rev Immunol, 28, 275-294.  
20017116 R.L.Rich, and D.G.Myszka (2010).
Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
  J Mol Recognit, 23, 1.  
20616724 S.A.Leddon, and A.J.Sant (2010).
Generation of MHC class II-peptide ligands for CD4 T-cell allorecognition of MHC class II molecules.
  Curr Opin Organ Transplant, 15, 505-511.  
20566715 S.Gras, Z.Chen, J.J.Miles, Y.C.Liu, M.J.Bell, L.C.Sullivan, L.Kjer-Nielsen, R.M.Brennan, J.M.Burrows, M.A.Neller, R.Khanna, A.W.Purcell, A.G.Brooks, J.McCluskey, J.Rossjohn, and S.R.Burrows (2010).
Allelic polymorphism in the T cell receptor and its impact on immune responses.
  J Exp Med, 207, 1555-1567.
PDB codes: 3mv7 3mv8 3mv9
20483993 S.R.Burrows, Z.Chen, J.K.Archbold, F.E.Tynan, T.Beddoe, L.Kjer-Nielsen, J.J.Miles, R.Khanna, D.J.Moss, Y.C.Liu, S.Gras, L.Kostenko, R.M.Brennan, C.S.Clements, A.G.Brooks, A.W.Purcell, J.McCluskey, and J.Rossjohn (2010).
Hard wiring of T cell receptor specificity for the major histocompatibility complex is underpinned by TCR adaptability.
  Proc Natl Acad Sci U S A, 107, 10608-10613.
PDB codes: 3kww 3kxf
20045355 T.Nitta, S.Murata, K.Sasaki, H.Fujii, A.M.Ripen, N.Ishimaru, S.Koyasu, K.Tanaka, and Y.Takahama (2010).
Thymoproteasome shapes immunocompetent repertoire of CD8+ T cells.
  Immunity, 32, 29-40.  
19299745 A.Udyavar, R.Alli, P.Nguyen, L.Baker, and T.L.Geiger (2009).
Subtle affinity-enhancing mutations in a myelin oligodendrocyte glycoprotein-specific TCR alter specificity and generate new self-reactivity.
  J Immunol, 182, 4439-4447.  
19592275 D.G.Pellicci, O.Patel, L.Kjer-Nielsen, S.S.Pang, L.C.Sullivan, K.Kyparissoudis, A.G.Brooks, H.H.Reid, S.Gras, I.S.Lucet, R.Koh, M.J.Smyth, T.Mallevaey, J.L.Matsuda, L.Gapin, J.McCluskey, D.I.Godfrey, and J.Rossjohn (2009).
Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors.
  Immunity, 31, 47-59.
PDB codes: 3he6 3he7 3huj
  20948629 D.M.Kranz (2009).
Two mechanisms that account for major histocompatibility complex restriction of T cells.
  F1000 Biol Rep, 1, 0.  
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
19262510 J.P.Scott-Browne, J.White, J.W.Kappler, L.Gapin, and P.Marrack (2009).
Germline-encoded amino acids in the alphabeta T-cell receptor control thymic selection.
  Nature, 458, 1043-1046.  
19148199 K.C.Garcia, J.J.Adams, D.Feng, and L.K.Ely (2009).
The molecular basis of TCR germline bias for MHC is surprisingly simple.
  Nat Immunol, 10, 143-147.  
19042022 K.D.Jensen, E.E.Sercarz, and C.R.Gabaglia (2009).
Altered peptide ligands can modify the Th2 T cell response to the immunodominant 161-175 peptide of LACK (Leishmania homolog for the receptor of activated C kinase).
  Mol Immunol, 46, 366-374.  
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.  
19699075 K.W.Wucherpfennig, M.J.Call, L.Deng, and R.Mariuzza (2009).
Structural alterations in peptide-MHC recognition by self-reactive T cell receptors.
  Curr Opin Immunol, 21, 590-595.  
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
19472182 Y.Chen, Y.Shi, H.Cheng, Y.Q.An, and G.F.Gao (2009).
Structural immunology and crystallography help immunologists see the immune system in action: how T and NK cells touch their ligands.
  IUBMB Life, 61, 579-590.  
18946038 A.Kosmrlj, A.K.Jha, E.S.Huseby, M.Kardar, and A.K.Chakraborty (2008).
How the thymus designs antigen-specific and self-tolerant T cell receptor sequences.
  Proc Natl Acad Sci U S A, 105, 16671-16676.  
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.  
18925396 J.Plum, M.De Smedt, G.Leclercq, T.Taghon, T.Kerre, and B.Vandekerckhove (2008).
Human intrathymic development: a selective approach.
  Semin Immunopathol, 30, 411-423.  
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.  
18678247 L.K.Ely, S.R.Burrows, A.W.Purcell, J.Rossjohn, and J.McCluskey (2008).
T-cells behaving badly: structural insights into alloreactivity and autoimmunity.
  Curr Opin Immunol, 20, 575-580.  
  18941216 L.L.Jones, L.A.Colf, J.D.Stone, K.C.Garcia, and D.M.Kranz (2008).
Distinct CDR3 conformations in TCRs determine the level of cross-reactivity for diverse antigens, but not the docking orientation.
  J Immunol, 181, 6255-6264.
PDB codes: 3e2h 3e3q
18456484 P.Marrack, K.Rubtsova, J.Scott-Browne, and J.W.Kappler (2008).
T cell receptor specificity for major histocompatibility complex proteins.
  Curr Opin Immunol, 20, 203-207.  
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.