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Yorodumi- PDB-8d9r: AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide me... -
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-Basic information
Entry | Database: PDB / ID: 8d9r | ||||||||||||
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Title | AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1 | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN/PROTEIN TRANSPORT / nef / AP / trafficking / VIRAL PROTEIN-PROTEIN TRANSPORT complex | ||||||||||||
Function / homology | Function and homology information basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / symbiont-mediated suppression of host T-cell mediated immune response / AP-1 adaptor complex / trans-Golgi Network Vesicle Budding / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis ...basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / symbiont-mediated suppression of host T-cell mediated immune response / AP-1 adaptor complex / trans-Golgi Network Vesicle Budding / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis / platelet dense granule organization / regulation of receptor internalization / protein trimerization / melanosome assembly / regulation of Arp2/3 complex-mediated actin nucleation / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / Golgi to lysosome transport / Intra-Golgi traffic / Golgi to vacuole transport / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / Synthesis of PIPs at the Golgi membrane / Golgi Associated Vesicle Biogenesis / GTP-dependent protein binding / suppression by virus of host autophagy / clathrin adaptor activity / MHC class II antigen presentation / melanosome organization / thioesterase binding / CD4 receptor binding / Nef Mediated CD4 Down-regulation / dendritic spine organization / determination of left/right symmetry / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / clathrin-coated vesicle / Lysosome Vesicle Biogenesis / clathrin binding / Golgi Associated Vesicle Biogenesis / positive regulation of natural killer cell mediated cytotoxicity / host cell Golgi membrane / cell leading edge / Synthesis of PIPs at the plasma membrane / kinesin binding / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / intracellular copper ion homeostasis / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / protein targeting / MHC class I protein binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / COPI-mediated anterograde transport / TAP binding / regulation of calcium-mediated signaling / clathrin-coated pit / vesicle-mediated transport / protection from natural killer cell mediated cytotoxicity / viral life cycle / 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 / MHC class II antigen presentation / detection of bacterium / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Neutrophil degranulation / T cell receptor binding / sarcomere / small monomeric GTPase / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / virion component / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / cytoplasmic vesicle membrane / trans-Golgi network / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / T cell mediated cytotoxicity / recycling endosome / antigen processing and presentation of endogenous peptide antigen via MHC class I / cellular response to virus / positive regulation of T cell cytokine production / MHC class I protein complex / small GTPase binding / 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 Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 20 Å | ||||||||||||
Authors | Hooy, R.M. / Hurley, J.H. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Sci Adv / Year: 2022 Title: Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat. Authors: Richard M Hooy / Yuichiro Iwamoto / Dan A Tudorica / Xuefeng Ren / James H Hurley / Abstract: The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to ...The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to sequester major histocompatibility complex class I (MHC-I), evading immune detection. We found that AP-1:Arf1:Nef:MHC-I forms a coat on tubulated membranes without clathrin and determined its structure. The coat assembles via Arf1 dimer interfaces. AP-1-positive tubules are enriched in cells upon clathrin knockdown. Nef localizes preferentially to AP-1 tubules in cells, explaining how Nef sequesters MHC-I. Coat contact residues are conserved across Arf isoforms and the Arf-dependent AP complexes AP-1, AP-3, and AP-4. Thus, AP complexes can self-assemble with Arf1 into tubular coats without clathrin or other scaffolding factors. The AP-1:Arf1 coat defines the structural basis of a broader class of tubulovesicular membrane coats as an intermediate in clathrin vesicle formation from internal membranes and as an MHC-I sequestration mechanism in HIV-1 infection. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d9r.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8d9r.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 8d9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/8d9r ftp://data.pdbj.org/pub/pdb/validation_reports/d9/8d9r | HTTPS FTP |
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-Related structure data
Related structure data | 27191MC 7ux3C 8d4cC 8d4dC 8d4eC 8d4fC 8d4gC 8d9sC 8d9tC 8d9uC 8d9vC 8d9wC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
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