Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat.
Journal, issue, pages	Sci Adv, Vol. 8, Issue 42, Page eadd3914, Year 2022
Publish date	Oct 21, 2022
Authors	Richard M Hooy / Yuichiro Iwamoto / Dan A Tudorica / Xuefeng Ren / James H Hurley /
PubMed 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.
External links	Sci Adv / PubMed:36269825 / PubMed Central
Methods	EM (subtomogram averaging)
Resolution	9.2 - 20.0 Å
Structure data	26853 7ux3 EMDB-26853, PDB-7ux3: Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes Method: EM (subtomogram averaging) / Resolution: 9.6 Å 27181 8d4c EMDB-27181, PDB-8d4c: beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes Method: EM (subtomogram averaging) / Resolution: 9.3 Å 27182 8d4d EMDB-27182, PDB-8d4d: gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes Method: EM (subtomogram averaging) / Resolution: 9.6 Å 27183 8d4e EMDB-27183, PDB-8d4e: Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Method: EM (subtomogram averaging) / Resolution: 9.2 Å 27184 8d4f EMDB-27184, PDB-8d4f: beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Method: EM (subtomogram averaging) / Resolution: 9.8 Å 27185 8d4g EMDB-27185, PDB-8d4g: gamma-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated wide(r) membrane tubes Method: EM (subtomogram averaging) / Resolution: 11.6 Å 27186 8d9w EMDB-27186: Beta-Arf1 homodimeric interface within AP-1 lattice on narrow membrane tubes PDB-8d9w: beta-Arf1 homodimeric interface within AP-1, Arf1, Nef, MHC-I lattice on narrow tubes Method: EM (subtomogram averaging) / Resolution: 9.3 Å 27187 8d9v EMDB-27187: Gamma-Arf1 homodimeric interface within AP-1 lattice on narrow membrane tubes PDB-8d9v: gamma-Arf1 homodimeric interface within AP-1, Arf1, Nef lattice on narrow membrane tubes Method: EM (subtomogram averaging) / Resolution: 9.4 Å 27188 8d9u EMDB-27188: Subtomogram average of AP-1, Arf1 and Nef complexes on narrow membrane tubes centered on beta-Arf1 dimers PDB-8d9u: AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on beta-Arf1 Method: EM (subtomogram averaging) / Resolution: 20.0 Å 27189 8d9t EMDB-27189: Subtomogram average of AP-1, Arf1 and Nef complexes on narrow membrane tubes centered on gamma-Arf1 dimers PDB-8d9t: AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on gamma-Arf1 Method: EM (subtomogram averaging) / Resolution: 20.0 Å 27190 8d9s EMDB-27190: Subtomogram average of AP-1, Arf1 and Nef complexes on wide(r) membrane tubes centered on beta-Arf1 dimers PDB-8d9s: AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on beta-Arf1 Method: EM (subtomogram averaging) / Resolution: 20.0 Å 27191 8d9r EMDB-27191: Subtomogram average of AP-1, Arf1 and Nef complexes on wide(r) membrane tubes centered on gamma-Arf1 dimers PDB-8d9r: AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1 Method: EM (subtomogram averaging) / Resolution: 20.0 Å
Chemicals	ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying moleculeYM / Guanosine triphosphate ChemComp-MG*: Unknown entry
Source	homo sapiens (human) human immunodeficiency virus 1 mus musculus (house mouse)
Keywords	VIRAL PROTEIN/PROTEIN TRANSPORT / nef / AP / HIV / trafficking / VIRAL PROTEIN / VIRAL PROTEIN-PROTEIN TRANSPORT complex / PROTEIN TRANSPORT / Protein Transport/Viral Protein / complex / coat / Protein Transport-Viral Protein complex