spacer
spacer
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Immune system PDB id
1duz
Jmol
Contents
Protein chains
275 a.a. *
100 a.a. *
Ligands
LEU-LEU-PHE-GLY-
TYR-PRO-VAL-TYR-
VAL ×2
Waters ×608
* Residue conservation analysis
PDB id:
1duz
Name: Immune system
Title: Human class i histocompatibility antigen (hla-a 0201) in complex with a nonameric peptide from htlv-1 tax protein
Structure: Hla-a 0201. Chain: a, d. Fragment: heavy chain. Engineered: yes. Beta-2 microglobulin. Chain: b, e. Engineered: yes. Htlv-1 octameric tax peptide. Chain: c, f.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: peptide was obtained through standard solid- phase peptide synthesis
Biol. unit: Trimer (from PQS)
Resolution:
1.80Å     R-factor:   0.198     R-free:   0.250
Authors: A.R.Khan,B.M.Baker,P.Ghosh,W.E.Biddison,D.C.Wiley
Key ref: A.R.Khan et al. (2000). The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site. J Immunol, 164, 6398-6405. PubMed id: 10843695 Ref: Full text
Date:
19-Jan-00     Release date:   04-Feb-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P01892  (1A02_HUMAN) -  HLA class I histocompatibility antigen, A-2 alpha chain
Seq:
Struc: 		365 a.a.
275 a.a.
Protein chains
Pfam   ArchSchema ?
P61769  (B2MG_HUMAN) -  Beta-2-microglobulin
Seq:
Struc: 		119 a.a.
100 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   8 terms 
  Biological process     immune response   8 terms 
  Biochemical function     protein binding     1 term  

 

 
Full text J Immunol 164:6398-6405 (2000)
PubMed id: 10843695  
 
 
The structure and stability of an HLA-A*0201/octameric tax peptide complex with an empty conserved peptide-N-terminal binding site.
A.R.Khan, B.M.Baker, P.Ghosh, W.E.Biddison, D.C.Wiley.
 
  ABSTRACT  
 
The crystal structure of the human class I MHC molecule HLA-A2 complexed with of an octameric peptide, Tax8 (LFGYPVYV), from human T cell lymphotrophic virus-1 (HTLV-1) has been determined. This structure is compared with a newly refined, higher resolution (1.8 A) structure of HLA-A2 complexed with the nonameric Tax9 peptide (LLFGYPVYV) with one more N-terminal residue. Despite the absence of a peptide residue (P1) bound in the conserved N-terminal peptide-binding pocket of the Tax8/HLA-A2 complex, the structures of the two complexes are essentially identical. Water molecules in the Tax8 complex replace the terminal amino group of the Tax9 peptide and mediate a network of hydrogen bonds among the secondary structural elements at that end of the peptide-binding groove. Thermal denaturation measurements indicate that the Tax8 complex is much less stable, DeltaTm = 16 degrees C, than the Tax9 complex, but both can sensitize target cells for lysis by some Tax-specific CTL from HTLV-1 infected individuals. The absence of a P1 peptide residue is thus not enough to prevent formation of a "closed conformation" of the peptide-binding site. TCR affinity measurements and cytotoxic T cell assays indicate that the Tax8/HLA-A2 complex does not functionally cross-react with the A6-TCR-bearing T cell clone specific for Tax9/HLA-A2 complexes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21131979 C.Liu, M.R.Sawaya, and D.Eisenberg (2011).
β₂-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages.
  Nat Struct Mol Biol, 18, 49-55.  
21543847 R.M.McMahon, L.Friis, C.Siebold, M.A.Friese, L.Fugger, and E.Y.Jones (2011).
Structure of HLA-A*0301 in complex with a peptide of proteolipid protein: insights into the role of HLA-A alleles in susceptibility to multiple sclerosis.
  Acta Crystallogr D Biol Crystallogr, 67, 447-454.  
20976198 I.K.Macdonald, M.Harkiolaki, L.Hunt, T.Connelley, A.V.Carroll, N.D.MacHugh, S.P.Graham, E.Y.Jones, W.I.Morrison, D.R.Flower, and S.A.Ellis (2010).
MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors.
  PLoS Pathog, 6, e1001149.  
20927455 M.Tarbe, I.Azcune, E.Balentová, J.J.Miles, E.E.Edwards, K.M.Miles, P.Do, B.M.Baker, A.K.Sewell, J.M.Aizpurua, C.Douat-Casassus, and S.Quideau (2010).
Design, synthesis and evaluation of β-lactam antigenic peptide hybrids; unusual opening of the β-lactam ring in acidic media.
  Org Biomol Chem, 8, 5345-5353.  
20088607 V.L.Mendoza, K.Antwi, M.A.Barón-Rodríguez, C.Blanco, and R.W.Vachet (2010).
Structure of the preamyloid dimer of beta-2-microglobulin from covalent labeling and mass spectrometry.
  Biochemistry, 49, 1522-1532.  
19772349 F.K.Insaidoo, J.Zajicek, and B.M.Baker (2009).
A general and efficient approach for NMR studies of peptide dynamics in class I MHC peptide binding grooves.
  Biochemistry, 48, 9708-9710.  
18575802 F.Tian, L.Yang, F.Lv, Q.Yang, and P.Zhou (2009).
In silico quantitative prediction of peptides binding affinity to human MHC molecule: an intuitive quantitative structure-activity relationship approach.
  Amino Acids, 36, 535-554.  
19119025 G.Dong, P.A.Wearsch, D.R.Peaper, P.Cresswell, and K.M.Reinisch (2009).
Insights into MHC class I peptide loading from the structure of the tapasin-ERp57 thiol oxidoreductase heterodimer.
  Immunity, 30, 21-32.
PDB code: 3f8u
19297351 H.Zhang, O.Lund, and M.Nielsen (2009).
The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding.
  Bioinformatics, 25, 1293-1299.  
19657763 N.H.Heegaard (2009).
beta(2)-microglobulin: from physiology to amyloidosis.
  Amyloid, 16, 151-173.  
20064447 O.Y.Borbulevych, K.H.Piepenbrink, B.E.Gloor, D.R.Scott, R.F.Sommese, D.K.Cole, A.K.Sewell, and B.M.Baker (2009).
T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility.
  Immunity, 31, 885-896.
PDB codes: 3h7b 3h9h 3h9s 3ixa
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
18841329 P.Zhou, X.Chen, and Z.Shang (2009).
Side-chain conformational space analysis (SCSA): A multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities.
  J Comput Aided Mol Des, 23, 129-141.  
19443191 R.Abele, and R.Tampé (2009).
Peptide trafficking and translocation across membranes in cellular signaling and self-defense strategies.
  Curr Opin Cell Biol, 21, 508-515.  
19696882 V.Castillo, and S.Ventura (2009).
Amyloidogenic regions and interaction surfaces overlap in globular proteins related to conformational diseases.
  PLoS Comput Biol, 5, e1000476.  
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.  
18493987 M.A.Exley, R.Hou, A.Shaulov, E.Tonti, P.Dellabona, G.Casorati, O.Akbari, H.O.Akman, E.A.Greenfield, J.E.Gumperz, J.E.Boyson, S.P.Balk, and S.B.Wilson (2008).
Selective activation, expansion, and monitoring of human iNKT cells with a monoclonal antibody specific for the TCR alpha-chain CDR3 loop.
  Eur J Immunol, 38, 1756-1766.  
19090919 P.Zhou, F.Tian, and Z.Shang (2008).
LigEvolutioner, a new strategy for modification and optimization of lead compounds in receptor/ligand complexes.
  Chem Biol Drug Des, 72, 525-532.  
17483158 H.D.White, and A.E.Ashcroft (2007).
Real-time measurement of myosin-nucleotide noncovalent complexes by electrospray ionization mass spectrometry.
  Biophys J, 93, 914-919.  
17449678 K.M.Armstrong, and B.M.Baker (2007).
A comprehensive calorimetric investigation of an entropically driven T cell receptor-peptide/major histocompatibility complex interaction.
  Biophys J, 93, 597-609.  
17332746 M.Chen, and M.Bouvier (2007).
Analysis of interactions in a tapasin/class I complex provides a mechanism for peptide selection.
  EMBO J, 26, 1681-1690.  
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
17719062 O.Y.Borbulevych, F.K.Insaidoo, T.K.Baxter, D.J.Powell, L.A.Johnson, N.P.Restifo, and B.M.Baker (2007).
Structures of MART-126/27-35 Peptide/HLA-A2 complexes reveal a remarkable disconnect between antigen structural homology and T cell recognition.
  J Mol Biol, 372, 1123-1136.
PDB codes: 2gt9 2gtw 2gtz 2guo
17057332 G.Røder, T.Blicher, S.Justesen, B.Johannesen, O.Kristensen, J.Kastrup, S.Buus, and M.Gajhede (2006).
Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype.
  Acta Crystallogr D Biol Crystallogr, 62, 1300-1310.
PDB codes: 1xr8 1xr9
16636995 S.L.Myers, N.H.Thomson, S.E.Radford, and A.E.Ashcroft (2006).
Investigating the structural properties of amyloid-like fibrils formed in vitro from beta2-microglobulin using limited proteolysis and electrospray ionisation mass spectrometry.
  Rapid Commun Mass Spectrom, 20, 1628-1636.  
16322574 S.Park, and J.G.Saven (2006).
Simulation of pH-dependent edge strand rearrangement in human beta-2 microglobulin.
  Protein Sci, 15, 200-207.  
16451209 Y.S.Heo, S.H.Hwang, O.J.Kwon, S.S.Hur, and H.B.Oh (2006).
Structural aspect of novel HLA-A*02 allele, A*0286, identified by sequence-based typing.
  Tissue Antigens, 67, 84-85.  
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
15886110 I.Van Rhijn, D.M.Zajonc, I.A.Wilson, and D.B.Moody (2005).
T-cell activation by lipopeptide antigens.
  Curr Opin Immunol, 17, 222-229.  
  15814707 O.Y.Borbulevych, T.K.Baxter, Z.Yu, N.P.Restifo, and B.M.Baker (2005).
Increased immunogenicity of an anchor-modified tumor-associated antigen is due to the enhanced stability of the peptide/MHC complex: implications for vaccine design.
  J Immunol, 174, 4812-4820.
PDB codes: 1tvb 1tvh
16181329 T.Elliott, and A.Williams (2005).
The optimization of peptide cargo bound to MHC class I molecules by the peptide-loading complex.
  Immunol Rev, 207, 89-99.  
15493870 C.A.Wright, P.Kozik, M.Zacharias, and S.Springer (2004).
Tapasin and other chaperones: models of the MHC class I loading complex.
  Biol Chem, 385, 763-778.  
15454423 M.Zacharias, and S.Springer (2004).
Conformational flexibility of the MHC class I alpha1-alpha2 domain in peptide bound and free states: a molecular dynamics simulation study.
  Biophys J, 87, 2203-2214.  
14523945 C.J.Cohen, G.Denkberg, A.Lev, M.Epel, and Y.Reiter (2003).
Recombinant antibodies with MHC-restricted, peptide-specific, T-cell receptor-like specificity: new tools to study antigen presentation and TCR-peptide-MHC interactions.
  J Mol Recognit, 16, 324-332.  
12119416 C.H.Trinh, D.P.Smith, A.P.Kalverda, S.E.Phillips, and S.E.Radford (2002).
Crystal structure of monomeric human beta-2-microglobulin reveals clues to its amyloidogenic properties.
  Proc Natl Acad Sci U S A, 99, 9771-9776.
PDB code: 1lds
12077441 L.Li, N.Promadej, J.M.McNicholl, and M.Bouvier (2002).
Crystallization and preliminary X-ray crystallographic studies of HLA-A*1101 complexed with an HIV-1 decapeptide.
  Acta Crystallogr D Biol Crystallogr, 58, 1195-1197.  
12445283 P.Romero, D.Valmori, M.J.Pittet, A.Zippelius, D.Rimoldi, F.Lévy, V.Dutoit, M.Ayyoub, V.Rubio-Godoy, O.Michielin, P.Guillaume, P.Batard, I.F.Luescher, F.Lejeune, D.Liénard, N.Rufer, P.Y.Dietrich, D.E.Speiser, and J.C.Cerottini (2002).
Antigenicity and immunogenicity of Melan-A/MART-1 derived peptides as targets for tumor reactive CTL in human melanoma.
  Immunol Rev, 188, 81-96.  
11967566 V.J.McParland, A.P.Kalverda, S.W.Homans, and S.E.Radford (2002).
Structural properties of an amyloid precursor of beta(2)-microglobulin.
  Nat Struct Biol, 9, 326-331.  
11391001 B.E.Gewurz, R.Gaudet, D.Tortorella, E.W.Wang, H.L.Ploegh, and D.C.Wiley (2001).
Antigen presentation subverted: Structure of the human cytomegalovirus protein US2 bound to the class I molecule HLA-A2.
  Proc Natl Acad Sci U S A, 98, 6794-6799.
PDB code: 1im3
11498300 B.E.Gewurz, R.Gaudet, D.Tortorella, E.W.Wang, and H.L.Ploegh (2001).
Virus subversion of immunity: a structural perspective.
  Curr Opin Immunol, 13, 442-450.  
11238586 B.M.Baker, R.V.Turner, S.J.Gagnon, D.C.Wiley, and W.E.Biddison (2001).
Identification of a crucial energetic footprint on the alpha1 helix of human histocompatibility leukocyte antigen (HLA)-A2 that provides functional interactions for recognition by tax peptide/HLA-A2-specific T cell receptors.
  J Exp Med, 193, 551-562.  
11536359 O.Schueler-Furman, Y.Altuvia, and H.Margalit (2001).
Examination of possible structural constraints of MHC-binding peptides by assessment of their native structure within their source proteins.
  Proteins, 45, 47-54.  
11070166 B.M.Baker, S.J.Gagnon, W.E.Biddison, and D.C.Wiley (2000).
Conversion of a T cell antagonist into an agonist by repairing a defect in the TCR/peptide/MHC interface: implications for TCR signaling.
  Immunity, 13, 475-484.  
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.