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Yorodumi- PDB-8d9v: gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice o... -
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Basic information
| Entry | Database: PDB / ID: 8d9v | ||||||||||||
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| Title | gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice on narrow membrane tubes | ||||||||||||
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Keywords | VIRAL PROTEIN / nef / AP / HIV / trafficking | ||||||||||||
| Function / homology | Function and homology informationbasolateral protein secretion / endosome to melanosome transport / Lysosome Vesicle Biogenesis / AP-1 adaptor complex / mitotic cleavage furrow ingression / protein trimerization / platelet dense granule organization / negative regulation of glycoprotein biosynthetic process / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / melanosome assembly ...basolateral protein secretion / endosome to melanosome transport / Lysosome Vesicle Biogenesis / AP-1 adaptor complex / mitotic cleavage furrow ingression / protein trimerization / platelet dense granule organization / negative regulation of glycoprotein biosynthetic process / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / melanosome assembly / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / Golgi Associated Vesicle Biogenesis / symbiont-mediated suppression of host autophagy / clathrin adaptor activity / symbiont-mediated suppression of host apoptosis / MHC class II antigen presentation / thioesterase binding / CD4 receptor binding / determination of left/right symmetry / clathrin-coated vesicle / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / 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 / clathrin binding / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / cell leading edge / endoplasmic reticulum exit site / MHC class I protein binding / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / host cell Golgi membrane / protection from natural killer cell mediated cytotoxicity / 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 / intracellular copper ion homeostasis / detection of bacterium / protein targeting / T cell receptor binding / vesicle-mediated transport / viral life cycle / clathrin-coated pit / regulation of calcium-mediated signaling / Neutrophil degranulation / MHC class II antigen presentation / cytoplasmic vesicle membrane / Nef mediated downregulation of MHC class I complex cell surface expression / sarcomere / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / kidney development / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / cellular response to virus / peptide antigen binding / SH3 domain binding / positive regulation of T cell mediated cytotoxicity / virion component / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / synaptic vesicle / antibacterial humoral response / protein transport / T cell receptor signaling pathway / presynapse / E3 ubiquitin ligases ubiquitinate target proteins / heart development / ER-Phagosome pathway / ATPase binding / early endosome membrane / early endosome / defense response to Gram-positive bacterium / immune response / symbiont-mediated suppression of host innate immune response / signaling receptor binding / Golgi membrane / protein domain specific binding / lysosomal membrane / innate immune response / external side of plasma membrane Similarity search - Function | ||||||||||||
| Biological species | Homo sapiens (human)![]() Human immunodeficiency virus 1![]() | ||||||||||||
| Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.4 Å | ||||||||||||
Authors | Hooy, R.M. / Hurley, J.H. | ||||||||||||
| Funding support | United States, 3items
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Citation | Journal: Sci Adv / Year: 2022Title: 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. | ||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 8d9v.cif.gz | 674.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb8d9v.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 8d9v.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 8d9v_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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| Full document | 8d9v_full_validation.pdf.gz | 1.3 MB | Display | |
| Data in XML | 8d9v_validation.xml.gz | 89.1 KB | Display | |
| Data in CIF | 8d9v_validation.cif.gz | 149 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/8d9v ftp://data.pdbj.org/pub/pdb/validation_reports/d9/8d9v | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 27187MC ![]() 7ux3C ![]() 8d4cC ![]() 8d4dC ![]() 8d4eC ![]() 8d4fC ![]() 8d4gC ![]() 8d9rC ![]() 8d9sC ![]() 8d9tC ![]() 8d9uC ![]() 8d9wC C: citing same article ( M: map data used to model this data |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Assembly
| Deposited unit | ![]()
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| Noncrystallographic symmetry (NCS) | NCS domain:
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About Yorodumi



Homo sapiens (human)
Human immunodeficiency virus 1

United States, 3items
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