PDBsum entry 2axh

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Immune system PDB id
Protein chains
242 a.a.
Waters ×90
PDB id:
Name: Immune system
Title: Crystal structures of t cell receptor beta chains related to rheumatoid arthritis
Structure: T cell receptor beta chain. Chain: a, b. Fragment: extracellular domain. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dodecamer (from PQS)
2.70Å     R-factor:   0.237     R-free:   0.280
Authors: H.Li,S.Van Vranken,Y.Zhao,Z.Li,Y.Guo,L.Eisele,Y.Li
Key ref:
H.Li et al. (2005). Crystal structures of T cell receptor (beta) chains related to rheumatoid arthritis. Protein Sci, 14, 3025-3038. PubMed id: 16260763 DOI: 10.1110/ps.051748305
05-Sep-05     Release date:   20-Sep-05    
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Protein chains
Pfam   ArchSchema ?
P01850  (TRBC1_HUMAN) -  T-cell receptor beta-1 chain C region
177 a.a.
242 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)


DOI no: 10.1110/ps.051748305 Protein Sci 14:3025-3038 (2005)
PubMed id: 16260763  
Crystal structures of T cell receptor (beta) chains related to rheumatoid arthritis.
H.Li, S.Van Vranken, Y.Zhao, Z.Li, Y.Guo, L.Eisele, Y.Li.
The crystal structures of the Vbeta17+ beta chains of two human T cell receptors (TCRs), originally derived from the synovial fluid (SF4) and tissue (C5-1) of a patient with rheumatoid arthritis (RA), have been determined in native (SF4) and mutant (C5-1(F104-->Y/C187-->S)) forms, respectively. These TCR beta chains form homo-dimers in solution and in crystals. Structural comparison reveals that the main-chain conformations in the CDR regions of the C5-1 and SF4 Vbeta17 closely resemble those of a Vbeta17 JM22 in a bound form; however, the CDR3 region shows different conformations among these three Vbeta17 structures. At the side-chain level, conformational differences were observed at the CDR2 regions between our two ligand-free forms and the bound JM22 form. Other significant differences were observed at the Vbeta regions 8-12, 40-44, and 82-88 between C5-1/SF4 and JM22 Vbeta17, implying that there is considerable variability in the structures of very similar beta chains. Structural alignments also reveal a considerable variation in the Vbeta-Cbeta associations, and this may affect ligand recognition. The crystal structures also provide insights into the structure basis of T cell recognition of Mycoplasma arthritidis mitogen (MAM), a superantigen that may be implicated in the development of human RA. Structural comparisons of the Vbeta domains of known TCR structures indicate that there are significant similarities among Vbeta regions that are MAM-reactive, whereas there appear to be significant structural differences among those Vbeta regions that lack MAM-reactivity. It further reveals that CDR2 and framework region (FR) 3 are likely to account for the binding of TCR to MAM.
  Selected figure(s)  
Figure 1.
Figure 1. Primary sequence alignment of the CDR3 regions (underlined) of three human V 17 TCR chains: V 17 SF4, C5-1, and JM22 (Stewart-Jones et al. 2003). Identical CDR3 residues are shaded.
Figure 2.
Figure 2. The structures of V 17 TCR chains. (A,B) Representative (2F[o] - F[c]) electron density maps, contoured at 1.0 , of the CDR3 regions of V 17C5-1[YS] (A) and V 17SF4 (B). (C,D) Ribbon diagram of the V 17C5-1[YS] homodimers in two possible associations. (C) Dimerization via V domains; (D) dimerization via C domains. The TCR V , C and CDR loops are labeled.
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 3025-3038) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19376221 H.Miyakawa, R.P.Mason, J.Jiang, and M.B.Kadiiska (2009).
Lipid-derived free radical production in superantigen-induced interstitial pneumonia.
  Free Radic Biol Med, 47, 241-249.  
18716897 Y.Ou, C.Tong, Y.Zhang, P.Cai, J.Gu, Y.Liu, H.Liu, H.Wang, B.Chu, and P.Zhu (2009).
An improved design of PCR primers for detection of human T cell receptor beta chain repertoire.
  Mol Biol Rep, 36, 145-152.  
17220897 L.Wang, Y.Zhao, Z.Li, Y.Guo, L.L.Jones, D.M.Kranz, W.Mourad, and H.Li (2007).
Crystal structure of a complete ternary complex of TCR, superantigen and peptide-MHC.
  Nat Struct Mol Biol, 14, 169-171.
PDB code: 2icw
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