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PDBsum entry 1mhc
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Histocompatibility antigen/peptide PDB id
1mhc

 

 

 

 

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Contents
Protein chains
276 a.a. *
99 a.a. *
Ligands
FME-TYR-PHE-ILE-
ASN-ILE-LEU-THR-
LEU ×2
NAG
Waters ×372
* Residue conservation analysis
PDB id:
1mhc
Name: Histocompatibility antigen/peptide
Title: Model of mhc class i h2-m3 with nonapeptide from rat nd1 refined at 2.3 angstroms resolution
Structure: Mhc class i antigen h2-m3. Chain: a, d. Synonym: major histocompatibility complex. Engineered: yes. Mutation: yes. Mhc class i antigen h2-m3. Chain: b, e. Synonym: major histocompatibility complex. Engineered: yes.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: h2-m3 b2m. Expressed in: drosophila melanogaster. Expression_system_taxid: 7227. Rattus rattus. Black rat. Organism_taxid: 10117
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.190    
Authors: C.-R.Wang,K.Fischer Lindahl,J.Deisenhofer
Key ref: C.R.Wang et al. (1995). Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3. Cell, 82, 655-664. PubMed id: 7664344 DOI: 10.1016/0092-8674(95)90037-3
Date:
23-Aug-95     Release date:   29-Jan-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q31093  (Q31093_MOUSE) -  Histocompatibility 2, M region locus 3 from Mus musculus
Seq:
Struc: 		336 a.a.
276 a.a.*
Protein chains
Pfam   ArchSchema ?
P01887  (B2MG_MOUSE) -  Beta-2-microglobulin from Mus musculus
Seq:
Struc: 		119 a.a.
99 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 

 
DOI no: 10.1016/0092-8674(95)90037-3 Cell 82:655-664 (1995)
PubMed id: 7664344  
 
 
Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3.
C.R.Wang, A.R.Castaño, P.A.Peterson, C.Slaughter, K.F.Lindahl, J.Deisenhofer.
 
  ABSTRACT  
 
H2-M3 is a class Ib MHC molecule of the mouse with a 10(4)-fold preference for binding N-formylated peptides. To elucidate the basis of this unusual specificity, we expressed and crystallized a soluble form of M3 with a formylated nonamer peptide, fMYFINILTL, and determined the structure by X-ray crystallography. M3, refined at 2.1 A resolution, resembles class la MHC molecules in its overall structure, but differs in the peptide-binding groove. The A pocket, which usually accommodates the free N-terminus of a bound peptide, is closed, and the peptide is shifted one residue, such that the P1 side chain is lodged in the B pocket. The formyl group is coordinated by His-9 and a bound water on the floor of the groove.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20162552 M.T.Chow, and H.S.Teh (2010).
H2-M3-restricted CD8+ T cells augment CD4+ T-cell responses by promoting DC maturation.
  Eur J Immunol, 40, 1408-1417.  
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
18304006 P.Marrack, J.P.Scott-Browne, S.Dai, L.Gapin, and J.W.Kappler (2008).
Evolutionarily conserved amino acids that control TCR-MHC interaction.
  Annu Rev Immunol, 26, 171-203.  
17537914 E.J.Adams, Z.S.Juo, R.T.Venook, M.J.Boulanger, H.Arase, L.L.Lanier, and K.C.Garcia (2007).
Structural elucidation of the m157 mouse cytomegalovirus ligand for Ly49 natural killer cell receptors.
  Proc Natl Acad Sci U S A, 104, 10128-10133.
PDB code: 2nyk
16476767 H.Xu, T.Chun, H.J.Choi, B.Wang, and C.R.Wang (2006).
Impaired response to Listeria in H2-M3-deficient mice reveals a nonredundant role of MHC class Ib-specific T cells in host defense.
  J Exp Med, 203, 449-459.  
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.  
16652110 L.Charrier, and D.Merlin (2006).
The oligopeptide transporter hPepT1: gateway to the innate immune response.
  Lab Invest, 86, 538-546.  
16461341 S.E.D'Orazio, C.A.Shaw, and M.N.Starnbach (2006).
H2-M3-restricted CD8+ T cells are not required for MHC class Ib-restricted immunity against Listeria monocytogenes.
  J Exp Med, 203, 383-391.  
15928678 J.R.Rodgers, and R.G.Cook (2005).
MHC class Ib molecules bridge innate and acquired immunity.
  Nat Rev Immunol, 5, 459-471.  
16025565 M.J.Rabiet, E.Huet, and F.Boulay (2005).
Human mitochondria-derived N-formylated peptides are novel agonists equally active on FPR and FPRL1, while Listeria monocytogenes-derived peptides preferentially activate FPR.
  Eur J Immunol, 35, 2486-2495.  
16089503 R.Olson, K.E.Huey-Tubman, C.Dulac, and P.J.Bjorkman (2005).
Structure of a pheromone receptor-associated MHC molecule with an open and empty groove.
  PLoS Biol, 3, e257.
PDB code: 1zs8
  14634106 A.Ploss, G.Lauvau, B.Contos, K.M.Kerksiek, P.D.Guirnalda, I.Leiner, L.L.Lenz, M.J.Bevan, and E.G.Pamer (2003).
Promiscuity of MHC class Ib-restricted T cell responses.
  J Immunol, 171, 5948-5955.  
12634786 E.Treiner, L.Duban, S.Bahram, M.Radosavljevic, V.Wanner, F.Tilloy, P.Affaticati, S.Gilfillan, and O.Lantz (2003).
Selection of evolutionarily conserved mucosal-associated invariant T cells by MR1.
  Nature, 422, 164-169.  
12628182 J.Loconto, F.Papes, E.Chang, L.Stowers, E.P.Jones, T.Takada, A.Kumánovics, K.Fischer Lindahl, and C.Dulac (2003).
Functional expression of murine V2R pheromone receptors involves selective association with the M10 and M1 families of MHC class Ib molecules.
  Cell, 112, 607-618.  
14638756 S.E.D'Orazio, M.Velasquez, N.R.Roan, O.Naveiras-Torres, and M.N.Starnbach (2003).
The Listeria monocytogenes lemA gene product is not required for intracellular infection or to activate fMIGWII-specific T cells.
  Infect Immun, 71, 6721-6727.  
12671000 T.Takada, A.Kumánovics, C.Amadou, M.Yoshino, E.P.Jones, M.Athanasiou, G.A.Evans, and K.Fischer Lindahl (2003).
Species-specific class I gene expansions formed the telomeric 1 mb of the mouse major histocompatibility complex.
  Genome Res, 13, 589-600.  
12594948 Y.Liu, Y.Xiong, O.V.Naidenko, J.H.Liu, R.Zhang, A.Joachimiak, M.Kronenberg, H.Cheroutre, E.L.Reinherz, and J.H.Wang (2003).
The crystal structure of a TL/CD8alphaalpha complex at 2.1 A resolution: implications for modulation of T cell activation and memory.
  Immunity, 18, 205-215.
PDB code: 1nez
12479822 A.Achour, J.Michaëlsson, R.A.Harris, J.Odeberg, P.Grufman, J.K.Sandberg, V.Levitsky, K.Kärre, T.Sandalova, and G.Schneider (2002).
A structural basis for LCMV immune evasion: subversion of H-2D(b) and H-2K(b) presentation of gp33 revealed by comparative crystal structure.Analyses.
  Immunity, 17, 757-768.
PDB codes: 1n59 1n5a
12150894 X.L.He, C.Radu, J.Sidney, A.Sette, E.S.Ward, and K.C.Garcia (2002).
Structural snapshot of aberrant antigen presentation linked to autoimmunity: the immunodominant epitope of MBP complexed with I-Au.
  Immunity, 17, 83-94.
PDB code: 1k2d
11369794 G.Lauvau, and E.G.Pamer (2001).
CD8 T cell detection of bacterial infection: sniffing for formyl peptides derived from Mycobacterium tuberculosis.
  J Exp Med, 193, F35-F39.  
11369792 T.Chun, N.V.Serbina, D.Nolt, B.Wang, N.M.Chiu, J.L.Flynn, and C.R.Wang (2001).
Induction of M3-restricted cytotoxic T lymphocyte responses by N-formylated peptides derived from Mycobacterium tuberculosis.
  J Exp Med, 193, 1213-1220.  
10859333 J.Yagüe, I.Alvarez, D.Rognan, M.Ramos, J.Vázquez, and J.A.de Castro (2000).
An N-acetylated natural ligand of human histocompatibility leukocyte antigen (HLA)-B39. Classical major histocompatibility complex class I proteins bind peptides with a blocked NH(2) terminus in vivo.
  J Exp Med, 191, 2083-2092.  
10727453 K.Shinkai, and R.M.Locksley (2000).
CD1, tuberculosis, and the evolution of major histocompatibility complex molecules.
  J Exp Med, 191, 907-914.  
10964257 M.J.Soloski, M.E.Szperka, A.Davies, and S.L.Wooden (2000).
Host immune response to intracellular bacteria: A role for MHC-linked class-Ib antigen-presenting molecules.
  Proc Soc Exp Biol Med, 224, 231-239.  
10748237 N.Chiang, I.M.Fierro, K.Gronert, and C.N.Serhan (2000).
Activation of lipoxin A(4) receptors by aspirin-triggered lipoxins and select peptides evokes ligand-specific responses in inflammation.
  J Exp Med, 191, 1197-1208.  
10897379 S.W.Dow, A.Roberts, J.Vyas, J.Rodgers, R.R.Rich, I.Orme, and T.A.Potter (2000).
Immunization with f-Met peptides induces immune reactivity against Mycobacterium tuberculosis.
  Tuber Lung Dis, 80, 5.  
10432283 K.M.Kerksiek, D.H.Busch, I.M.Pilip, S.E.Allen, and E.G.Pamer (1999).
H2-M3-restricted T cells in bacterial infection: rapid primary but diminished memory responses.
  J Exp Med, 190, 195-204.  
10607669 K.Maenaka, and E.Y.Jones (1999).
MHC superfamily structure and the immune system.
  Curr Opin Struct Biol, 9, 745-753.  
10468588 M.He, L.Wen, C.E.Campbell, J.Y.Wu, and Y.Rao (1999).
Transcription repression by Xenopus ET and its human ortholog TBX3, a gene involved in ulnar-mammary syndrome.
  Proc Natl Acad Sci U S A, 96, 10212-10217.  
10601361 N.M.Chiu, B.Wang, K.M.Kerksiek, R.Kurlander, E.G.Pamer, and C.R.Wang (1999).
The selection of M3-restricted T cells is dependent on M3 expression and presentation of N-formylated peptides in the thymus.
  J Exp Med, 190, 1869-1878.  
10430630 N.M.Chiu, T.Chun, M.Fay, M.Mandal, and C.R.Wang (1999).
The majority of H2-M3 is retained intracellularly in a peptide-receptive state and traffics to the cell surface in the presence of N-formylated peptides.
  J Exp Med, 190, 423-434.  
10523605 O.V.Naidenko, J.K.Maher, W.A.Ernst, T.Sakai, R.L.Modlin, and M.Kronenberg (1999).
Binding and antigen presentation of ceramide-containing glycolipids by soluble mouse and human CD1d molecules.
  J Exp Med, 190, 1069-1080.  
10429675 Q.R.Fan, and D.C.Wiley (1999).
Structure of human histocompatibility leukocyte antigen (HLA)-Cw4, a ligand for the KIR2D natural killer cell inhibitory receptor.
  J Exp Med, 190, 113-123.
PDB code: 1qqd
10435577 R.E.Berg, M.F.Princiotta, S.Irion, J.A.Moticka, K.R.Dahl, and U.D.Staerz (1999).
Positive selection of an H2-M3 restricted T cell receptor.
  Immunity, 11, 33-43.  
10047540 V.M.Braud, D.S.Allan, and A.J.McMichael (1999).
Functions of nonclassical MHC and non-MHC-encoded class I molecules.
  Curr Opin Immunol, 11, 100-108.  
9597133 E.Pamer, and P.Cresswell (1998).
Mechanisms of MHC class I--restricted antigen processing.
  Annu Rev Immunol, 16, 323-358.  
9523114 I.A.Wilson, and P.J.Bjorkman (1998).
Unusual MHC-like molecules: CD1, Fc receptor, the hemochromatosis gene product, and viral homologs.
  Curr Opin Immunol, 10, 67-73.  
9584149 M.F.Princiotta, L.L.Lenz, M.J.Bevan, and U.D.Staerz (1998).
H2-M3 restricted presentation of a Listeria-derived leader peptide.
  J Exp Med, 187, 1711-1719.  
9643627 P.J.Fairchild (1998).
Presentation of antigenic peptides by products of the major histocompatibility complex.
  J Pept Sci, 4, 182-194.  
9842920 V.M.Dabhi, and K.F.Lindahl (1998).
Short peptides sensitize target cells to CTL specific for the MHC class Ib molecule, H2-M3.
  Eur J Immunol, 28, 3773-3782.  
9730898 Z.Kurepa, C.A.Hasemann, and J.Forman (1998).
Qa-1b binds conserved class I leader peptides derived from several mammalian species.
  J Exp Med, 188, 973-978.  
9314081 E.G.Pamer, A.J.Sijts, M.S.Villanueva, D.H.Busch, and S.Vijh (1997).
MHC class I antigen processing of Listeria monocytogenes proteins: implications for dominant and subdominant CTL responses.
  Immunol Rev, 158, 129-136.  
9368774 E.Simpson, and D.Roopenian (1997).
Minor histocompatibility antigens.
  Curr Opin Immunol, 9, 655-661.  
9039778 E.Y.Jones (1997).
MHC class I and class II structures.
  Curr Opin Immunol, 9, 75-79.  
9283291 I.Torrini, M.Paglialunga Paradisi, G.Pagani Zecchini, G.Lucente, E.Gavuzzo, F.Mazza, G.Pochetti, S.Traniello, and S.Spisani (1997).
Synthesis, conformation, and biological activity of two fMLP-OMe analogues containing the new 2-[2'-(methylthio)ethyl]methionine residue.
  Biopolymers, 42, 415-426.  
9287185 J.K.Maher, and M.Kronenberg (1997).
The role of CD1 molecules in immune responses to infection.
  Curr Opin Immunol, 9, 456-461.  
9287179 J.Reimann, and S.H.Kaufmann (1997).
Alternative antigen processing pathways in anti-infective immunity.
  Curr Opin Immunol, 9, 462-469.  
9143709 K.F.Lindahl, D.E.Byers, V.M.Dabhi, R.Hovik, E.P.Jones, G.P.Smith, C.R.Wang, H.Xiao, and M.Yoshino (1997).
H2-M3, a full-service class Ib histocompatibility antigen.
  Annu Rev Immunol, 15, 851-879.  
9314079 L.L.Lenz, and M.J.Bevan (1997).
CTL responses to H2-M3-restricted Listeria epitopes.
  Immunol Rev, 158, 115-121.  
9354467 L.M.Mendoza, P.Paz, A.Zuberi, G.Christianson, D.Roopenian, and N.Shastri (1997).
Minors held by majors: the H13 minor histocompatibility locus defined as a peptide/MHC class I complex.
  Immunity, 7, 461-472.  
9316393 M.A.Batalia, and E.J.Collins (1997).
Peptide binding by class I and class II MHC molecules.
  Biopolymers, 43, 281-302.  
9314080 R.Kurlander, and C.Nataraj (1997).
Characterization of the murine H2-M3wt-restricted CD8 response against a hydrophobic, protease-resistant, phospholipid-associated antigen from Listeria monocytogenes.
  Immunol Rev, 158, 123-128.  
9207006 R.P.Johnson (1997).
Upregulation of Fas ligand by simian immunodeficiency virus - a nef-arious mechanism of immune evasion?
  J Exp Med, 186, 1-5.  
9023340 S.Kim, J.G.Na, M.Hampsey, and D.Reinberg (1997).
The Dr1/DRAP1 heterodimer is a global repressor of transcription in vivo.
  Proc Natl Acad Sci U S A, 94, 820-825.  
9219685 Z.Zeng, A.R.Castaño, B.W.Segelke, E.A.Stura, P.A.Peterson, and I.A.Wilson (1997).
Crystal structure of mouse CD1: An MHC-like fold with a large hydrophobic binding groove.
  Science, 277, 339-345.
PDB code: 1cd1
8729450 A.Melián, E.M.Beckman, S.A.Porcelli, and M.B.Brenner (1996).
Antigen presentation by CD1 and MHC-encoded class I-like molecules.
  Curr Opin Immunol, 8, 82-88.  
8729452 D.H.Fremont, W.A.Rees, and H.Kozono (1996).
Biophysical studies of T-cell receptors and their ligands.
  Curr Opin Immunol, 8, 93.  
8820567 D.M.Ojcius, G.Gachelin, and A.Dautry-Varsat (1996).
Presentation of antigens derived from microorganisms residing in host-cell vacuoles.
  Trends Microbiol, 4, 53-59.  
8624811 K.J.Smith, S.W.Reid, D.I.Stuart, A.J.McMichael, E.Y.Jones, and J.I.Bell (1996).
An altered position of the alpha 2 helix of MHC class I is revealed by the crystal structure of HLA-B*3501.
  Immunity, 4, 203-213.
PDB code: 1a1n
8758895 L.L.Lenz, B.Dere, and M.J.Bevan (1996).
Identification of an H2-M3-restricted Listeria epitope: implications for antigen presentation by M3.
  Immunity, 5, 63-72.  
8662082 M.D.Crew, L.M.Bates, C.A.Douglass, and J.L.York (1996).
Expressed Peromyscus maniculatus (Pema) MHC class I genes: evolutionary implications and the identification of a gene encoding a Qa1-like antigen.
  Immunogenetics, 44, 177-185.  
8758896 P.H.Gulden, P.Fischer, N.E.Sherman, W.Wang, V.H.Engelhard, J.Shabanowitz, D.F.Hunt, and E.G.Pamer (1996).
A Listeria monocytogenes pentapeptide is presented to cytolytic T lymphocytes by the H2-M3 MHC class Ib molecule.
  Immunity, 5, 73-79.  
7584149 N.Lee, A.R.Malacko, A.Ishitani, M.C.Chen, J.Bajorath, H.Marquardt, and D.E.Geraghty (1995).
The membrane-bound and soluble forms of HLA-G bind identical sets of endogenous peptides but differ with respect to TAP association.
  Immunity, 3, 591-600.  
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 codes are shown on the right.

 

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