- PDB-4emz: HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adapti... -
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Basic information
Entry
Database: PDB / ID: 4emz
Title
HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain)
Components
AP-1 complex subunit mu-1
MHC-I
Protein Nef
Keywords
VIRAL PROTEIN/IMMUNE SYSTEM / Human immunodeficiency virus 1 / HIV / Nef / MHC-I / antigen presentation / host defense / Adaptor protein complex 1 / Mu1 adaptin subunit / sorting motif recognition / CLASP / membrane trafficking / viral hijacking / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information
perturbation by virus of host immune response / negative regulation of CD4 production / endosome to melanosome transport / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization / melanosome assembly / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host apoptosis ...perturbation by virus of host immune response / negative regulation of CD4 production / endosome to melanosome transport / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization / melanosome assembly / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / Golgi Associated Vesicle Biogenesis / clathrin adaptor activity / suppression by virus of host autophagy / MHC class II antigen presentation / CD4 receptor binding / thioesterase binding / clathrin-coated vesicle / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / host cell Golgi membrane / MHC class I protein binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / vesicle-mediated transport / regulation of calcium-mediated signaling / viral life cycle / Neutrophil degranulation / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / virion component / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / trans-Golgi network / MHC class I peptide loading complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / SH3 domain binding / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / Interferon alpha/beta signaling / positive regulation of type II interferon production / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / ER-Phagosome pathway / early endosome membrane / ATPase binding / antibacterial humoral response / early endosome / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / signaling receptor binding / endoplasmic reticulum membrane / GTP binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / Golgi apparatus / cell surface / endoplasmic reticulum / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol Similarity search - Function
Nef Regulatory Factor / Nef Regulatory Factor / Mu homology domain, subdomain B / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site ...Nef Regulatory Factor / Nef Regulatory Factor / Mu homology domain, subdomain B / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / AP-1 complex subunit mu-1 / Protein Nef Similarity search - Component
Biological species
Human immunodeficiency virus 1 Homo sapiens (human) Mus musculus (house mouse)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
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