Structure of the transporter associated with antigen processing trapped by herpes simplex virus

The transporter associated with antigen processing (TAP) is an ATP-binding cassette (ABC) transporter essential to cellular immunity against viral infection. Some persistent viruses have evolved strategies to inhibit TAP so that they may go undetected by the immune system. The herpes simplex virus for example evades immune surveillance by blocking peptide transport with a small viral protein ICP47. In this study, we determined the structure of human TAP bound to ICP47 by electron cryo-microscopy (cryo-EM) to 4.0 Å. The structure shows that ICP47 traps TAP in an inactive conformation distinct from the normal transport cycle. The specificity and potency of ICP47 inhibition result from contacts between the tip of the helical hairpin and the apex of the transmembrane cavity. This work provides a clear molecular description of immune evasion by a persistent virus. It also establishes the molecular structure of TAP to facilitate mechanistic studies of the antigen presentation process. DOI: http://dx.doi.org/10.7554/eLife.21829.001

[1]  T. Eyck,et al.  Efficient structure-factor calculation for large molecules by the fast Fourier transform , 1977 .

[2]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[3]  D. Wiley,et al.  Identification of domain boundaries within the N‐termini of TAP1 and TAP2 and their importance in tapasin binding and tapasin‐mediated increase in peptide loading of MHC class I , 2005, Immunology and cell biology.

[4]  J. Neefjes,et al.  Peptide size selection by the major histocompatibility complex-encoded peptide transporter , 1994, The Journal of experimental medicine.

[5]  N. Grigorieff,et al.  Optimal noise reduction in 3D reconstructions of single particles using a volume-normalized filter. , 2012, Journal of structural biology.

[6]  R. Demars,et al.  A gene in the human major histocompatibility complex class II region controlling the class I antigen presentation pathway , 1990, Nature.

[7]  A. Steven,et al.  One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. , 2013, Journal of structural biology.

[8]  I. Wilson,et al.  Crystal structures of two rat MHC class Ia (RT1-A) molecules that are associated differentially with peptide transporter alleles TAP-A and TAP-B. , 2002, Journal of molecular biology.

[9]  Sjors H. W. Scheres,et al.  An atomic structure of human γ-secretase , 2015, Nature.

[10]  Günter J. Hämmerling,et al.  Selectivity of MHC-encoded peptide transporters from human, mouse and rat , 1994, Nature.

[11]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2007, Current protocols in protein science.

[12]  N Grigorieff,et al.  Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 A in ice. , 1998, Journal of molecular biology.

[13]  P. A. Peterson,et al.  Molecular mechanism and species specificity of TAP inhibition by herpes simplex virus ICP47. , 1996, The EMBO journal.

[14]  J. Yewdell,et al.  Herpes simplex virus turns off the TAP to evade host immunity , 1995, Nature.

[15]  R. Obst,et al.  Analysis of the fine specificity of rat, mouse and human TAP peptide transporters , 1995, European journal of immunology.

[16]  N. Grigorieff,et al.  Quantitative characterization of electron detectors for transmission electron microscopy. , 2013, Journal of structural biology.

[17]  D. Y. Lin,et al.  Crystal structures of a polypeptide processing and secretion transporter , 2015, Nature.

[18]  K. Früh,et al.  A point mutation in the human transporter associated with antigen processing (TAP2) alters the peptide transport specificity , 1996, European journal of immunology.

[19]  S. Beck,et al.  Sequences encoded in the class II region of the MHC related to the 'ABC' superfamily of transporters , 1990, Nature.

[20]  J. Monaco,et al.  Transport protein genes in the murine MHC: possible implications for antigen processing. , 1990, Science.

[21]  S. Tonegawa,et al.  Peptide length and sequence specificity of the mouse TAP1/TAP2 translocator , 1994, The Journal of experimental medicine.

[22]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[23]  F. Momburg,et al.  O496 - Residues in TAP peptide transporters controlling substrate specificity , 1996 .

[24]  D. Andrews,et al.  A cytosolic herpes simplex virus protein inhibits antigen presentation to CD8+ T lymphocytes , 1994, Cell.

[25]  D. R. Madden,et al.  Identification of self peptides bound to purified HLA-B27 , 1991, Nature.

[26]  P. Cresswell,et al.  Human transporters associated with antigen processing possess a promiscuous peptide-binding site. , 1994, Immunity.

[27]  J. Monaco,et al.  MHC class II region encoding proteins related to the muKidrug resistance family of transmembrane transporters , 1990, Nature.

[28]  Rachelle Gaudet,et al.  Structure of the ABC ATPase domain of human TAP1, the transporter associated with antigen processing , 2001, The EMBO journal.

[29]  A. Barr,et al.  Structures of ABCB10, a human ATP-binding cassette transporter in apo- and nucleotide-bound states , 2013, Proceedings of the National Academy of Sciences.

[30]  C. Harding,et al.  Pathways of antigen processing. , 1991, Current opinion in immunology.

[31]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[32]  J. Drijfhout,et al.  Inhibition of mouse TAP by immune evasion molecules encoded by non-murine herpesviruses. , 2011, Molecular immunology.

[33]  A Leith,et al.  SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. , 1996, Journal of structural biology.

[34]  Garib N. Murshudov,et al.  Conformation-independent structural comparison of macromolecules with ProSMART , 2014, Acta crystallographica. Section D, Biological crystallography.

[35]  R. F. Cook,et al.  The Active Site of ICP47, a Herpes Simplex Virus–encoded Inhibitor of the Major Histocompatibility Complex (MHC)-encoded Peptide Transporter Associated with Antigen Processing (TAP), Maps to the NH2-terminal 35 Residues , 1997, The Journal of experimental medicine.

[36]  M. Nijenhuis,et al.  Multiple regions of the transporter associated with antigen processing (TAP) contribute to its peptide binding site. , 1996, Journal of immunology.

[37]  H. Rammensee,et al.  SYFPEITHI: database for MHC ligands and peptide motifs , 1999, Immunogenetics.

[38]  R. Henderson,et al.  Detective quantum efficiency of electron area detectors in electron microscopy , 2009, Ultramicroscopy.

[39]  Marcus A. Brubaker,et al.  Alignment of cryo-EM movies of individual particles by optimization of image translations. , 2014, Journal of structural biology.

[40]  I. Pogozheva,et al.  Use of Functional Polymorphisms To Elucidate the Peptide Binding Site of TAP Complexes , 2015, The Journal of Immunology.

[41]  David N Mastronarde,et al.  Automated electron microscope tomography using robust prediction of specimen movements. , 2005, Journal of structural biology.

[42]  O. Jardetzky,et al.  Simple Allosteric Model for Membrane Pumps , 1966, Nature.

[43]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[44]  F. Momburg,et al.  Residues in TAP2 peptide transporters controlling substrate specificity. , 1996, Journal of immunology.

[45]  T. Walz,et al.  A mechanism of viral immune evasion revealed by cryo-EM analysis of the TAP transporter , 2015, Nature.

[46]  A Sette,et al.  The peptide-binding motif for the human transporter associated with antigen processing , 1995, The Journal of experimental medicine.

[47]  R. Henderson,et al.  Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. , 1992, Science.

[48]  J. Howard,et al.  Functional analysis by site-directed mutagenesis of the complex polymorphism in rat transporter associated with antigen processing. , 1998, Journal of immunology.

[49]  R. Tampé,et al.  Direct evidence that the N-terminal extensions of the TAP complex act as autonomous interaction scaffolds for the assembly of the MHC I peptide-loading complex , 2012, Cellular and Molecular Life Sciences.

[50]  H. Rammensee,et al.  Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules , 1991, Nature.

[51]  D. Andrews,et al.  Stable binding of the herpes simplex virus ICP47 protein to the peptide binding site of TAP. , 1996, The EMBO journal.

[52]  D. Agard,et al.  Electron counting and beam-induced motion correction enable near atomic resolution single particle cryoEM , 2013, Nature Methods.

[53]  R. Read,et al.  The crystal structure of pertussis toxin. , 1994, Structure.

[54]  H. Ploegh,et al.  Inhibition of Major Histocompatibility Complex Class I Antigen Presentation in Pig and Primate Cells by Herpes Simplex Virus Type 1 and 2 ICP47 , 1998, Journal of Virology.

[55]  R. Tampé,et al.  Assembly and Function of the Major Histocompatibility Complex (MHC) I Peptide-loading Complex Are Conserved Across Higher Vertebrates* , 2014, The Journal of Biological Chemistry.

[56]  Nir London,et al.  The structural basis of peptide-protein binding strategies. , 2010, Structure.

[57]  Alan Brown,et al.  Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions , 2015, Acta crystallographica. Section D, Biological crystallography.

[58]  R. Tampé,et al.  The active domain of the herpes simplex virus protein ICP47: a potent inhibitor of the transporter associated with antigen processing. , 1997, Journal of molecular biology.

[59]  Wen Jiang,et al.  EMAN2: an extensible image processing suite for electron microscopy. , 2007, Journal of structural biology.

[60]  N Grigorieff,et al.  Frealign: An Exploratory Tool for Single-Particle Cryo-EM. , 2016, Methods in enzymology.

[61]  S. Iwata,et al.  Structure of an antibacterial peptide ATP-binding cassette transporter in a novel outward occluded state , 2014, Proceedings of the National Academy of Sciences.

[62]  Nikolaus Grigorieff,et al.  Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6 , 2015, eLife.

[63]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[64]  J. Neefjes,et al.  Selective and ATP-dependent translocation of peptides by the MHC-encoded transporter. , 1993, Science.

[65]  N. Grigorieff,et al.  CTFFIND4: Fast and accurate defocus estimation from electron micrographs , 2015, bioRxiv.

[66]  P. A. Peterson,et al.  A viral inhibitor of peptide transporters for antigen presentation , 1995, Nature.

[67]  S. Tonegawa,et al.  TAP1-dependent peptide translocation in vitro is ATP dependent and peptide selective , 1993, Cell.

[68]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.

[69]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[70]  Jue Chen,et al.  Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans , 2012 .

[71]  Sjors H.W. Scheres,et al.  RELION: Implementation of a Bayesian approach to cryo-EM structure determination , 2012, Journal of structural biology.

[72]  C. Robinson,et al.  Structural and Functional Basis for Lipid Synergy on the Activity of the Antibacterial Peptide ABC Transporter McjD* , 2016, The Journal of Biological Chemistry.