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

 

 

 

 

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Contents
Protein chains
276 a.a. *
100 a.a. *
Ligands
ARG-ARG
LYS-TRP-ARG-ARG-
TRP
HIS-LEU
GOL ×5
Metals
_MN
Waters ×721
* Residue conservation analysis
PDB id:
1ogt
Name: Immune system
Title: Crystal structure of hla-b 2705 Complexed with the vasoactive intestinal peptide type 1 receptor (vipr) peptide (residues 400-408)
Structure: Hla class i histocompatibility antigen. Chain: a. Fragment: extracellular domain, residues 25-300. Synonym: b-27 b 2705 Alpha chain, human leucocyte antigen b 2705 Heavy chain. Engineered: yes. Beta-2-microglobulin. Chain: b. Fragment: residues 21-119.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this peptide was chemically synthesised
Biol. unit: Trimer (from PDB file)
Resolution:
1.47Å     R-factor:   0.131     R-free:   0.178
Authors: M.Hulsmeyer,M.T.Fiorillo,F.Bettosini,R.Sorrentino,W.Saenger, A.Ziegler,B.Uchanska-Ziegler
Key ref: M.Hülsmeyer et al. (2004). Dual, HLA-B27 subtype-dependent conformation of a self-peptide. J Exp Med, 199, 271-281. PubMed id: 14734527
Date:
13-May-03     Release date:   29-Jan-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P01889  (1B07_HUMAN) -  HLA class I histocompatibility antigen, B alpha chain from Homo sapiens
Seq:
Struc: 		362 a.a.
276 a.a.*
Protein chain
P61769  (B2MG_HUMAN) -  Beta-2-microglobulin from Homo sapiens
Seq:
Struc: 		119 a.a.
100 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 21 residue positions (black crosses)

 

 
J Exp Med 199:271-281 (2004)
PubMed id: 14734527  
 
 
Dual, HLA-B27 subtype-dependent conformation of a self-peptide.
M.Hülsmeyer, M.T.Fiorillo, F.Bettosini, R.Sorrentino, W.Saenger, A.Ziegler, B.Uchanska-Ziegler.
 
  ABSTRACT  
 
The products of the human leukocyte antigen subtypes HLA-B*2705 and HLA-B*2709 differ only in residue 116 (Asp vs. His) within the peptide binding groove but are differentially associated with the autoimmune disease ankylosing spondylitis (AS); HLA-B*2705 occurs in AS-patients, whereas HLA-B*2709 does not. The subtypes also generate differential T cell repertoires as exemplified by distinct T cell responses against the self-peptide pVIPR (RRKWRRWHL). The crystal structures described here show that pVIPR binds in an unprecedented dual conformation only to HLA-B*2705 molecules. In one binding mode, peptide pArg5 forms a salt bridge to Asp116, connected with drastically different interactions between peptide and heavy chain, contrasting with the second, conventional conformation, which is exclusively found in the case of B*2709. These subtype-dependent differences in pVIPR binding link the emergence of dissimilar T cell repertoires in individuals with HLA-B*2705 or HLA-B*2709 to the buried Asp116/His116 polymorphism and provide novel insights into peptide presentation by major histocompatibility antigens.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21280120 B.Loll, C.Rückert, C.S.Hee, W.Saenger, B.Uchanska-Ziegler, and A.Ziegler (2011).
Loss of recognition by cross-reactive T cells and its relation to a C-terminus-induced conformational reorientation of an HLA-B*2705-bound peptide.
  Protein Sci, 20, 278-290.
PDB code: 3lv3
  21414141 H.Fabian, B.Loll, H.Huser, D.Naumann, B.Uchanska-Ziegler, and A.Ziegler (2011).
Influence of inflammation-related changes on conformational characteristics of HLA-B27 subtypes as detected by IR spectroscopy.
  FEBS J, 278, 1713-1727.  
20457890 B.R.Jordan (2010).
Cloning and sequencing the first HLA gene.
  Genetics, 184, 879-886.  
21151886 C.S.Hee, S.Gao, B.Loll, M.M.Miller, B.Uchanska-Ziegler, O.Daumke, and A.Ziegler (2010).
Structure of a classical MHC class I molecule that binds "non-classical" ligands.
  PLoS Biol, 8, e1000557.
PDB codes: 3p73 3p77
20532195 E.B.Unal, A.Gursoy, and B.Erman (2010).
VitAL: Viterbi algorithm for de novo peptide design.
  PLoS One, 5, e10926.  
20131248 H.Fabian, H.Huser, B.Loll, A.Ziegler, D.Naumann, and B.Uchanska-Ziegler (2010).
HLA-B27 heavy chains distinguished by a micropolymorphism exhibit differential flexibility.
  Arthritis Rheum, 62, 978-987.  
20112362 J.A.López de Castro (2010).
The HLA-B27 peptidome: building on the cornerstone.
  Arthritis Rheum, 62, 316-319.  
20517295 L.S.Tam, J.Gu, and D.Yu (2010).
Pathogenesis of ankylosing spondylitis.
  Nat Rev Rheumatol, 6, 399-405.  
20541422 P.Kumar, A.Ziegler, A.Grahn, C.S.Hee, and A.Ziegler (2010).
Leaving the structural ivory tower, assisted by interactive 3D PDF.
  Trends Biochem Sci, 35, 419-422.  
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
20628622 T.Haliloglu, A.Gul, and B.Erman (2010).
Predicting important residues and interaction pathways in proteins using Gaussian Network Model: binding and stability of HLA proteins.
  PLoS Comput Biol, 6, e1000845.  
19201651 A.Ziegler, C.A.Müller, R.A.Böckmann, and B.Uchanska-Ziegler (2009).
Low-affinity peptides and T-cell selection.
  Trends Immunol, 30, 53-60.  
19620307 M.Honda, R.Wang, W.P.Kong, M.Kanekiyo, W.Akahata, L.Xu, K.Matsuo, K.Natarajan, H.Robinson, T.E.Asher, D.A.Price, D.C.Douek, D.H.Margulies, and G.J.Nabel (2009).
Different vaccine vectors delivering the same antigen elicit CD8+ T cell responses with distinct clonotype and epitope specificity.
  J Immunol, 183, 2425-2434.
PDB codes: 3e6f 3e6h
19617632 P.Kumar, A.Vahedi-Faridi, W.Saenger, E.Merino, J.A.López de Castro, B.Uchanska-Ziegler, and A.Ziegler (2009).
Structural basis for T cell alloreactivity among three HLA-B14 and HLA-B27 antigens.
  J Biol Chem, 284, 29784-29797.
PDB codes: 3bp4 3bp7 3bvn 3bxn
18486928 A.Mathieu, A.Cauli, M.T.Fiorillo, and R.Sorrentino (2008).
HLA-B27 and ankylosing spondylitis geographic distribution as the result of a genetic selection induced by malaria endemic? A review supporting the hypothesis.
  Autoimmun Rev, 7, 398-403.  
18668120 F.Paladini, E.Cocco, A.Cauli, I.Cascino, A.Vacca, F.Belfiore, M.T.Fiorillo, A.Mathieu, and R.Sorrentino (2008).
A functional polymorphism of the vasoactive intestinal peptide receptor 1 gene correlates with the presence of HLA-B*2705 in Sardinia.
  Genes Immun, 9, 659-667.  
18489433 M.Marcilla, and J.A.López de Castro (2008).
Peptides: the cornerstone of HLA-B27 biology and pathogenetic role in spondyloarthritis.
  Tissue Antigens, 71, 495-506.  
17665402 A.Cauli, A.Vacca, A.Mameli, G.Passiu, M.T.Fiorillo, R.Sorrentino, and A.Mathieu (2007).
A Sardinian patient with ankylosing spondylitis and HLA-B*2709 co-occurring with HLA-B*1403.
  Arthritis Rheum, 56, 2807-2809.  
17665395 I.Cascino, F.Paladini, F.Belfiore, A.Cauli, C.Angelini, M.T.Fiorillo, A.Mathieu, and R.Sorrentino (2007).
Identification of previously unrecognized predisposing factors for ankylosing spondylitis from analysis of HLA-B27 extended haplotypes in Sardinia.
  Arthritis Rheum, 56, 2640-2651.  
17665436 I.Olivieri, S.D'Angelo, E.Scarano, V.Santospirito, and A.Padula (2007).
The HLA-B*2709 subtype in a woman with early ankylosing spondylitis.
  Arthritis Rheum, 56, 2805-2807.  
17665431 J.D.Taurog (2007).
The mystery of HLA-B27: if it isn't one thing, it's another.
  Arthritis Rheum, 56, 2478-2481.  
17289555 M.A.Khan, A.Mathieu, R.Sorrentino, and N.Akkoc (2007).
The pathogenetic role of HLA-B27 and its subtypes.
  Autoimmun Rev, 6, 183-189.  
18083574 M.Koch, S.Camp, T.Collen, D.Avila, J.Salomonsen, H.J.Wallny, A.van Hateren, L.Hunt, J.P.Jacob, F.Johnston, D.A.Marston, I.Shaw, P.R.Dunbar, V.Cerundolo, E.Y.Jones, and J.Kaufman (2007).
Structures of an MHC class I molecule from B21 chickens illustrate promiscuous peptide binding.
  Immunity, 27, 885-899.
PDB codes: 3bev 3bew
  17620730 P.Kumar, A.Vahedi-Faridi, E.Merino, J.A.López de Castro, A.Volz, A.Ziegler, W.Saenger, and B.Uchanska-Ziegler (2007).
Expression, purification and preliminary X-ray crystallographic analysis of the human major histocompatibility antigen HLA-B*1402 in complex with a viral peptide and with a self-peptide.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 631-634.  
16932724 H.Gaston (2006).
Mechanisms of Disease: the immunopathogenesis of spondyloarthropathies.
  Nat Clin Pract Rheumatol, 2, 383-392.  
16783853 P.Gómez, V.Montserrat, M.Marcilla, A.Paradela, and J.A.de Castro (2006).
B*2707 differs in peptide specificity from B*2705 and B*2704 as much as from HLA-B27 subtypes not associated to spondyloarthritis.
  Eur J Immunol, 36, 1867-1881.  
  16511044 B.Loll, A.Zawacka, J.Biesiadka, C.Rückert, A.Volz, W.Saenger, B.Uchanska-Ziegler, and A.Ziegler (2005).
Purification, crystallization and preliminary X-ray diffraction analysis of the human major histocompatibility antigen HLA-B*2703 complexed with a viral peptide and with a self-peptide.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 372-374.  
15578174 C.Roos, and L.Walter (2005).
Considerable haplotypic diversity in the RT1-CE class I gene region of the rat major histocompatibility complex.
  Immunogenetics, 56, 773-777.  
15771591 E.S.Trombetta, and I.Mellman (2005).
Cell biology of antigen processing in vitro and in vivo.
  Annu Rev Immunol, 23, 975.  
16275762 F.E.Tynan, D.Elhassen, A.W.Purcell, J.M.Burrows, N.A.Borg, J.J.Miles, N.A.Williamson, K.J.Green, J.Tellam, L.Kjer-Nielsen, J.McCluskey, J.Rossjohn, and S.R.Burrows (2005).
The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound conformation.
  J Exp Med, 202, 1249-1260.
PDB codes: 2axf 2axg
16200572 F.Paladini, E.Taccari, M.T.Fiorillo, A.Cauli, G.Passiu, A.Mathieu, L.Punzi, G.Lapadula, R.Scarpa, and R.Sorrentino (2005).
Distribution of HLA-B27 subtypes in Sardinia and continental Italy and their association with spondylarthropathies.
  Arthritis Rheum, 52, 3319-3321.  
16181344 S.B.Lovitch, and E.R.Unanue (2005).
Conformational isomers of a peptide-class II major histocompatibility complex.
  Immunol Rev, 207, 293-313.  
14734520 K.W.Wucherpfennig (2004).
Presentation of a self-peptide in two distinct conformations by a disease-associated HLA-B27 subtype.
  J Exp Med, 199, 151-154.  
15573121 R.Horton, L.Wilming, V.Rand, R.C.Lovering, E.A.Bruford, V.K.Khodiyar, M.J.Lush, S.Povey, C.C.Talbot, M.W.Wright, H.M.Wain, J.Trowsdale, A.Ziegler, and S.Beck (2004).
Gene map of the extended human MHC.
  Nat Rev Genet, 5, 889-899.  
15469407 S.H.Shoshan, and A.Admon (2004).
MHC-bound antigens and proteomics for novel target discovery.
  Pharmacogenomics, 5, 845-859.  
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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