[English] 日本語
Yorodumi- PDB-8d9r: AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d9r | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1 | ||||||||||||
Components |
| ||||||||||||
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 / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization ...basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization / Glycosphingolipid transport / regulation of receptor internalization / 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 / Intra-Golgi traffic / Golgi to vacuole transport / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / symbiont-mediated suppression of host apoptosis / Synthesis of PIPs at the Golgi membrane / Golgi Associated Vesicle Biogenesis / clathrin adaptor activity / suppression by virus of host autophagy / MHC class II antigen presentation / CD4 receptor binding / Nef Mediated CD4 Down-regulation / thioesterase binding / dendritic spine organization / determination of left/right symmetry / long-term synaptic depression / clathrin-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / 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 / clathrin binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / Golgi Associated Vesicle Biogenesis / CD8 receptor binding / cell leading edge / MHC class I protein binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / host cell Golgi membrane / endoplasmic reticulum exit site / Synthesis of PIPs at the plasma membrane / 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 / intracellular copper ion homeostasis / protein targeting / beta-2-microglobulin binding / COPI-mediated anterograde transport / T cell receptor binding / detection of bacterium / clathrin-coated pit / vesicle-mediated transport / regulation of calcium-mediated signaling / viral life cycle / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Neutrophil degranulation / sarcomere / small monomeric GTPase / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / 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 / cytoplasmic vesicle membrane / 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 / cellular response to virus / 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 / heart development / T cell receptor signaling pathway / ER-Phagosome pathway 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
| ||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8d9r.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
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
Summary document | 8d9r_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8d9r_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 8d9r_validation.xml.gz | 254.7 KB | Display | |
Data in CIF | 8d9r_validation.cif.gz | 432.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/8d9r ftp://data.pdbj.org/pub/pdb/validation_reports/d9/8d9r | HTTPS FTP |
-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 |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
|