|Entry||Database: EMDB / ID: EMD-7454|
|Title||Structure of the HIV-Nef dileucine mutant bound AP-1:Arf1 dimer|
|Sample||Dimeric assembly of AP-1:Arf1:Tetherin-Nef dileucine (LL164-165AA) mutant|
|Function / homology|
Function and homology information
negative regulation of intracellular transport of viral material / negative regulation of plasmacytoid dendritic cell cytokine production / phospholipase D activator activity / mitotic cleavage furrow ingression / Golgi to transport vesicle transport / synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / negative regulation of CD4 biosynthetic process ...negative regulation of intracellular transport of viral material / negative regulation of plasmacytoid dendritic cell cytokine production / phospholipase D activator activity / mitotic cleavage furrow ingression / Golgi to transport vesicle transport / synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / negative regulation of CD4 biosynthetic process / suppression by symbiont of host T-cell mediated immune response / positive regulation of leukocyte proliferation / AP-1 adaptor complex / regulation of Arp2/3 complex-mediated actin nucleation / clathrin adaptor complex / positive regulation of natural killer cell degranulation / positive regulation of ER to Golgi vesicle-mediated transport / endosome to melanosome transport / Golgi to lysosome transport / response to interferon-beta / very-low-density lipoprotein particle assembly / melanosome organization / regulation of receptor internalization / suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I / response to interferon-alpha / COPI-coated vesicle / postsynaptic actin cytoskeleton organization / suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host adaptive immune response / metalloendopeptidase inhibitor activity / membrane coat / suppression by virus of host autophagy / positive regulation of calcium ion-dependent exocytosis / dendritic spine organization / GTP-dependent protein binding / positive regulation of natural killer cell mediated cytotoxicity / long-term synaptic depression / CD4 receptor binding / determination of left/right symmetry / thioesterase binding / regulation of calcium-mediated signaling / azurophil granule membrane / peroxisomal membrane / host cell Golgi membrane / clathrin binding / positive regulation of endocytosis / positive regulation of dendritic spine development / clathrin-coated vesicle / kinesin binding / response to interferon-gamma / MHC class I protein binding / B cell activation / cell leading edge / positive regulation of sodium ion transmembrane transport / negative regulation of viral genome replication / phosphatidylinositol biosynthetic process / cellular copper ion homeostasis / trans-Golgi network membrane / protein targeting / clathrin-coated pit / Rab GTPase binding / clathrin-coated vesicle membrane / cellular response to virus / antigen processing and presentation of exogenous peptide antigen via MHC class II / anchored component of membrane / regulation of actin cytoskeleton organization / negative regulation of cell migration / positive regulation of protein secretion / sarcomere / actin filament organization / multivesicular body / vesicle-mediated transport / collagen binding / microtubule cytoskeleton organization / interleukin-12-mediated signaling pathway / response to virus / microtubule cytoskeleton / GDP binding / recycling endosome / cytoplasmic vesicle membrane / type I interferon signaling pathway / intracellular protein transport / trans-Golgi network / virion / regulation of defense response to virus by virus / viral life cycle / SH3 domain binding / negative regulation of cell growth / lysosomal membrane / late endosome / defense response to virus / apical plasma membrane / heart development / ATPase binding / positive regulation of I-kappaB kinase/NF-kappaB signaling / protein C-terminus binding / postsynaptic density / GTPase activity / neuron projection / Golgi membrane
Clathrin adaptor, mu subunit / AP complex, mu/sigma subunit / Beta-adaptin appendage, C-terminal subdomain / Clathrin adaptor, appendage, Ig-like subdomain superfamily / HIV negative factor Nef / Clathrin adaptor complex, small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / TBP domain superfamily / Armadillo-like helical ...Clathrin adaptor, mu subunit / AP complex, mu/sigma subunit / Beta-adaptin appendage, C-terminal subdomain / Clathrin adaptor, appendage, Ig-like subdomain superfamily / HIV negative factor Nef / Clathrin adaptor complex, small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / TBP domain superfamily / Armadillo-like helical / Adaptor protein complex, sigma subunit / Small GTP-binding protein domain / Adaptor protein complex AP-1, gamma subunit / Clathrin adaptor, mu subunit, conserved site / Small GTPase superfamily, ARF/SAR type / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / AP-1/2/4 complex subunit beta / Armadillo / Gamma-adaptin ear (GAE) domain / Bone marrow stromal antigen 2 / AP complex subunit beta / P-loop containing nucleoside triphosphate hydrolase / HIV-1 Nef protein, anchor domain superfamily / HIV-1 Nef protein, core domain superfamily / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Mu homology domain / Longin-like domain superfamily / AP-2 complex subunit mu, C-terminal superfamily / Armadillo-type fold
AP-1 complex subunit gamma-1 / AP-1 complex subunit mu-1 / ADP-ribosylation factor 1 / AP-1 complex subunit beta-1 / Bone marrow stromal antigen 2 / Protein Nef / AP-1 complex subunit sigma-3
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 6.72 Å|
|Authors||Buffalo CZ / Morris KL / Hurley JH|
|Citation||Journal: Cell / Year: 2018|
Title: HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation.
Authors: Kyle L Morris / Cosmo Z Buffalo / Christina M Stürzel / Elena Heusinger / Frank Kirchhoff / Xuefeng Ren / James H Hurley /
Abstract: The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 Å cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, ...The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 Å cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, HIV-1 Nef, and the cytosolic tail of the restriction factor tetherin suggested a mechanism for inactivating tetherin by Golgi retention. The 4.3 Å structure of a mutant Nef-induced dimer of AP-1 showed how the closed trimer is regulated by the dileucine loop of Nef. HDX-MS and mutational analysis were used to show how cargo dynamics leads to alternative Arf1 trimerization, directing Nef targets to be either retained at the trans-Golgi or sorted to lysosomes. Phosphorylation of the NL4-3 M-Nef was shown to regulate AP-1 trimerization, explaining how O-Nefs lacking this phosphosite counteract tetherin but most M-Nefs do not. These observations show how the higher-order organization of a vesicular coat can be allosterically modulated to direct cargoes to distinct fates.
|Validation Report||PDB-ID: 6d84|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_7454.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.067 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Dimeric assembly of AP-1:Arf1:Tetherin-Nef dileucine (LL164-165AA...
|Entire||Name: Dimeric assembly of AP-1:Arf1:Tetherin-Nef dileucine (LL164-165AA) mutant|
Number of components: 1
-Component #1: protein, Dimeric assembly of AP-1:Arf1:Tetherin-Nef dileucine (LL...
|Protein||Name: Dimeric assembly of AP-1:Arf1:Tetherin-Nef dileucine (LL164-165AA) mutant|
Recombinant expression: No
|Mass||Theoretical: 470 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.7 mg/mL|
Buffer solution: 20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 294 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 39.7 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 22500.0 X (nominal), 46849.0 X (calibrated) / Cs: 2.6 mm / Imaging mode: BRIGHT FIELD / Defocus: 750.0 - 2500.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 1989|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 42902|
|3D reconstruction||Software: RELION / Resolution: 6.72 Å / Resolution method: FSC 0.143 CUT-OFF|
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