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PDBsum entry 1m05
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protein ligands metals Protein-protein interface(s) links
Immune system PDB id
1m05

 

 

 

 

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Contents
Protein chains
269 a.a. *
99 a.a. *
Ligands
PHE-LEU-ARG-GLY-
ARG-ALA-TYR-GLY-
LEU ×2
Metals
_CD ×2
Waters ×794
* Residue conservation analysis
PDB id:
1m05
Name: Immune system
Title: Hla b8 in complex with an epstein barr virus determinant
Structure: Hla class i histocompatibility antigen, b-8 b 0801 Alpha chain. Chain: a, c. Fragment: residues 25-301. Engineered: yes. Other_details: truncation mutant. Beta-2-microglobulin. Chain: b, d. Fragment: residues 21-119.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence of the protein is naturally found in epstein-barr virus.
Biol. unit: Trimer (from PQS)
Resolution:
1.90Å     R-factor:   0.242     R-free:   0.283
Authors: L.Kjer-Nielsen,C.S.Clements,A.G.Brooks,A.W.Purcell,M.R.Fontes, J.Mccluskey,J.Rossjohn
Key ref: L.Kjer-Nielsen et al. (2002). The structure of HLA-B8 complexed to an immunodominant viral determinant: peptide-induced conformational changes and a mode of MHC class I dimerization. J Immunol, 169, 5153-5160. PubMed id: 12391232
Date:
11-Jun-02     Release date:   02-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P01889  (1B07_HUMAN) -  HLA class I histocompatibility antigen, B alpha chain from Homo sapiens
Seq:
Struc: 		362 a.a.
269 a.a.*
Protein chains
Pfam   ArchSchema ?
P61769  (B2MG_HUMAN) -  Beta-2-microglobulin from Homo sapiens
Seq:
Struc: 		119 a.a.
99 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 

 
J Immunol 169:5153-5160 (2002)
PubMed id: 12391232  
 
 
The structure of HLA-B8 complexed to an immunodominant viral determinant: peptide-induced conformational changes and a mode of MHC class I dimerization.
L.Kjer-Nielsen, C.S.Clements, A.G.Brooks, A.W.Purcell, M.R.Fontes, J.McCluskey, J.Rossjohn.
 
  ABSTRACT  
 
EBV is a ubiquitous human pathogen that chronically infects up to 90% of the population. Persistent viral infection is characterized by latency and periods of viral replication that are kept in check by a strong antiviral CTL response. Despite the size of the EBV genome, CTL immunity focuses on only a few viral determinants but expands a large primary and memory response toward these epitopes. In unrelated HLA-B8(+) individuals, the response to the immunodominant latent Ag FLRGRAYGL from Epstein Barr nuclear Ag 3A is largely comprised of CTL clones with identical conserved alphabeta TCR structures. To better understand the structural correlates of Ag immunodominance and TCR selection bias, we have solved the crystal structure of the HLA-B8-FLRGRAYGL peptide complex to a resolution of 1.9 A. The structure confirms the importance of P3-Arg, P5-Arg, and P9-Leu as dominant anchor residues involved in peptide binding to HLA-B8. A bulged conformation of the bound peptide provides a structural basis for the critical role of the P7-Tyr residue in T cell recognition. The peptide also induces backbone and side-chain conformational changes in HLA-B8 that are transmitted along the peptide-binding groove in a domino effect. The HLA-B8-FLRGRAYGL complex crystallizes as a dimer in the asymmetric unit and is oriented such that both peptide ligands are projected in the same plane suggesting a higher order arrangement of MHC-peptide complexes that could be involved in formation of the class I Ag-loading complex or in T cell activation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23051753 L.Kjer-Nielsen, O.Patel, A.J.Corbett, J.Le Nours, B.Meehan, L.Liu, M.Bhati, Z.Chen, L.Kostenko, R.Reantragoon, N.A.Williamson, A.W.Purcell, N.L.Dudek, M.J.McConville, R.A.O'Hair, G.N.Khairallah, D.I.Godfrey, D.P.Fairlie, J.Rossjohn, and J.McCluskey (2012).
MR1 presents microbial vitamin B metabolites to MAIT cells.
  Nature, 491, 717-723.
PDB code: 4gup
20946353 S.Cho, J.Ryoo, Y.Jun, and K.Ahn (2011).
Receptor-mediated ER export of human MHC class I molecules is regulated by the C-terminal single amino acid.
  Traffic, 12, 42-55.  
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.  
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
19177349 P.Kumar, A.Vahedi-Faridi, W.Saenger, A.Ziegler, and B.Uchanska-Ziegler (2009).
Conformational changes within the HLA-A1:MAGE-A1 complex induced by binding of a recombinant antibody fragment with TCR-like specificity.
  Protein Sci, 18, 37-49.
PDB code: 3bo8
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
18378495 J.K.Archbold, W.A.Macdonald, S.R.Burrows, J.Rossjohn, and J.McCluskey (2008).
T-cell allorecognition: a case of mistaken identity or déjà vu?
  Trends Immunol, 29, 220-226.  
18301425 V.Venturi, D.A.Price, D.C.Douek, and M.P.Davenport (2008).
The molecular basis for public T-cell responses?
  Nat Rev Immunol, 8, 231-238.  
17603487 P.A.Wearsch, and P.Cresswell (2007).
Selective loading of high-affinity peptides onto major histocompatibility complex class I molecules by the tapasin-ERp57 heterodimer.
  Nat Immunol, 8, 873-881.  
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.  
17109469 C.S.Hourigan, M.Harkiolaki, N.A.Peterson, J.I.Bell, E.Y.Jones, and C.A.O'Callaghan (2006).
The structure of the human allo-ligand HLA-B*3501 in complex with a cytochrome p450 peptide: steric hindrance influences TCR allo-recognition.
  Eur J Immunol, 36, 3288-3293.
PDB code: 2cik
17116886 J.Racape, F.Connan, J.Hoebeke, J.Choppin, and J.G.Guillet (2006).
Influence of dominant HIV-1 epitopes on HLA-A3/peptide complex formation.
  Proc Natl Acad Sci U S A, 103, 18208-18213.  
16860610 L.C.Sullivan, H.L.Hoare, J.McCluskey, J.Rossjohn, and A.G.Brooks (2006).
A structural perspective on MHC class Ib molecules in adaptive immunity.
  Trends Immunol, 27, 413-420.  
16617112 L.K.Ely, T.Beddoe, C.S.Clements, J.M.Matthews, A.W.Purcell, L.Kjer-Nielsen, J.McCluskey, and J.Rossjohn (2006).
Disparate thermodynamics governing T cell receptor-MHC-I interactions implicate extrinsic factors in guiding MHC restriction.
  Proc Natl Acad Sci U S A, 103, 6641-6646.  
16774548 S.H.Hwang, Y.S.Lim, O.J.Kwon, Y.S.Heo, and H.B.Oh (2006).
Structural aspects of the B*3564 molecule, a novel HLA-B*35 allele identified by sequence-based typing.
  Tissue Antigens, 68, 90-91.  
17130450 V.Venturi, K.Kedzierska, D.A.Price, P.C.Doherty, D.C.Douek, S.J.Turner, and M.P.Davenport (2006).
Sharing of T cell receptors in antigen-specific responses is driven by convergent recombination.
  Proc Natl Acad Sci U S A, 103, 18691-18696.  
15718280 C.S.Clements, L.Kjer-Nielsen, L.Kostenko, H.L.Hoare, M.A.Dunstone, E.Moses, K.Freed, A.G.Brooks, J.Rossjohn, and J.McCluskey (2005).
Crystal structure of HLA-G: a nonclassical MHC class I molecule expressed at the fetal-maternal interface.
  Proc Natl Acad Sci U S A, 102, 3360-3365.
PDB code: 1ydp
15871015 L.Li, W.Chen, and M.Bouvier (2005).
A biochemical and structural analysis of genetic diversity within the HLA-A*11 subtype.
  Immunogenetics, 57, 315-325.  
15640805 N.A.Borg, L.K.Ely, T.Beddoe, W.A.Macdonald, H.H.Reid, C.S.Clements, A.W.Purcell, L.Kjer-Nielsen, J.J.Miles, S.R.Burrows, J.McCluskey, and J.Rossjohn (2005).
The CDR3 regions of an immunodominant T cell receptor dictate the 'energetic landscape' of peptide-MHC recognition.
  Nat Immunol, 6, 171-180.  
15496207 B.Hoppe, G.A.Heymann, C.Schoenemann, M.Nagy, H.Kiesewetter, and A.Salama (2004).
Description of a novel HLA-B allele, B*5613, identified during HLA-typing using sequence-specific oligonucleotide hybridization and sequence-specific amplification.
  Tissue Antigens, 64, 616-618.  
15181931 P.H.Atkinson (2004).
Glycosylation of prion strains in transmissible spongiform encephalopathies.
  Aust Vet J, 82, 292-299.  
12803494 A.W.Purcell, W.Zeng, N.A.Mifsud, L.K.Ely, W.A.Macdonald, and D.C.Jackson (2003).
Dissecting the role of peptides in the immune response: theory, practice and the application to vaccine design.
  J Pept Sci, 9, 255-281.  
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
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.

 

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