PDBsum entry 1zhb

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Immune system PDB id
Protein chains
273 a.a. *
99 a.a. *
Waters ×109
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Crystal structure of the murine class i major histocompatibility complex of h-2db, b2-microglobulin, and a 9-residue peptide derived from rat dopamine beta- monooxigenase
Structure: H-2 class i histocompatibility antigen, d-b alpha chain. Chain: a, d, g, j. Fragment: extracellular part. Synonym: h- 2db. Engineered: yes. Beta-2-microglobulin. Chain: b, e, h, k. Engineered: yes.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: h2-d. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: b2m. Synthetic: yes. Other_details: the peptide was chemically synthesized.
Biol. unit: Trimer (from PQS)
2.70Å     R-factor:   0.226     R-free:   0.262
Authors: T.Sandalova,J.Michaelsson,R.A.Harris,J.Odeberg,G.Schneider, K.Karre,A.Achour
Key ref:
T.Sandalova et al. (2005). A structural basis for CD8+ T cell-dependent recognition of non-homologous peptide ligands: implications for molecular mimicry in autoreactivity. J Biol Chem, 280, 27069-27075. PubMed id: 15845547 DOI: 10.1074/jbc.M500927200
25-Apr-05     Release date:   14-Jun-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P01899  (HA11_MOUSE) -  H-2 class I histocompatibility antigen, D-B alpha chain
362 a.a.
273 a.a.
Protein chains
Pfam   ArchSchema ?
P01887  (B2MG_MOUSE) -  Beta-2-microglobulin
119 a.a.
99 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   10 terms 
  Biological process     immune system process   13 terms 
  Biochemical function     protein binding     3 terms  


DOI no: 10.1074/jbc.M500927200 J Biol Chem 280:27069-27075 (2005)
PubMed id: 15845547  
A structural basis for CD8+ T cell-dependent recognition of non-homologous peptide ligands: implications for molecular mimicry in autoreactivity.
T.Sandalova, J.Michaëlsson, R.A.Harris, J.Odeberg, G.Schneider, K.Kärre, A.Achour.
Molecular mimicry of self-epitopes by viral antigens is one possible pathogenic mechanism underlying induction of autoimmunity. A self-epitope, mDBM, derived from mouse dopamine beta-mono-oxygenase (KALYDYAPI) sharing 44% sequence identity with the lymphocytic choriomeningitis virus-derived immunodominant epitope gp33 (KAVYNFATC/M), has previously been identified as a cross-reactive self-ligand, presentation of which results in autoimmunity. A rat peptide homologue, rDBM (KALYNYAPI, 56% identity to gp33), which displayed similar properties to mDBM, has also been identified. We herein report the crystal structure of H-2Db.rDBM and a comparison with the crystal structures of the cross-reactive H-2Db.gp33 and non-cross-reactive H-2Db.gp33 (V3L) escape variant (KALYNFATM, 88% identity to gp33). Despite the large sequence disparity, rDBM and gp33 peptides are presented in nearly identical manners by H-2Db, with a striking juxtaposition of the central sections of both peptides from residues p3 to p7. The structural similarity provides H-2Db in complex with either a virus-derived or a dopamine beta-mono-oxygenase-derived peptide with a shared antigenic identity that conserves the positioning of the heavy chain and peptide residues that interact with the T cell receptor (TCR). This stands in contrast to the structure of H-2Db.gp33 (V3L), in which a single conserved mutation, also present in rDBM, induces large movements of both the peptide backbone and the side chains that interact with the TCR. The TCR-interacting surfaces of the H-2Db.rDBM and H-2Db.gp33 major histocompatibility complexes are very similar with regard to shape, topology, and charge distribution, providing a structural basis for CD8 T cell activation by molecular mimicry and potential subsequent development of autoreactivity.
  Selected figure(s)  
Figure 1.
FIG. 1. Electron density map for the dopamine -mono-oxygenase-derived rDBM and the LCMV-derived gp33 peptides. Annealed omit 2F[o] - F[c] electron density maps of gp33 (top panel) and rDBM (bottom panel) when bound to H-2D^b contoured at 1.0 . The peptides are depicted with their N termini to the left and their C termini to the right, and the anchor positions are indicated by vertical arrows.
Figure 4.
FIG. 4. The surfaces of the H-2D^b·rDBM and H-2D^b·gp33 MHC class I complexes are similar. The TCR-interacting surfaces of H-2D^b in complex with either LCMV-derived gp33 peptide (top panel)or the rDBM peptide (bottom panel) are depicted (as viewed from above). The localizations of peptide residues that point up toward the peptide, as well as those of several H-2D^b residues known to play an important role in the interaction with TCR, are indicated. Negatively charged regions of the surface are shown in red, and positively charged regions are shown in blue, with a scale from -15 to +15 kiloteslas. This figure was created using the Grasp program (68).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 27069-27075) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20442757 D.A.Antunes, G.F.Vieira, M.M.Rigo, S.P.Cibulski, M.Sinigaglia, and J.A.Chies (2010).
Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC:peptide complexes to cross-reactivity assessment.
  PLoS One, 5, e10353.  
18509089 S.J.Lin, A.T.Chen, and R.M.Welsh (2008).
Immune system derived from homeostatic proliferation generates normal CD8 T-cell memory but altered repertoires and diminished heterologous immune responses.
  Blood, 112, 680-689.  
17485515 A.Peixoto, C.Evaristo, I.Munitic, M.Monteiro, A.Charbit, B.Rocha, and H.Veiga-Fernandes (2007).
CD8 single-cell gene coexpression reveals three different effector types present at distinct phases of the immune response.
  J Exp Med, 204, 1193-1205.  
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