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- EMDB-7453: Structure of the HIV-Nef dileucine mutant bound AP-1:Arf1 dimer m... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7453 | |||||||||
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Title | Structure of the HIV-Nef dileucine mutant bound AP-1:Arf1 dimer monomeric subunit | |||||||||
![]() | AP-1:Arf1:Tetherin-Nef dileucine mutant dimer monomeric subunit | |||||||||
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Function / homology | ![]() negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / 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 ...negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / 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 / response to interferon-alpha / 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 / metalloendopeptidase inhibitor activity / 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 / symbiont-mediated suppression of host apoptosis / clathrin adaptor activity / suppression by virus of host autophagy / MHC class II antigen presentation / positive regulation of leukocyte proliferation / 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 / azurophil granule membrane / clathrin binding / negative regulation of viral genome replication / Golgi Associated Vesicle Biogenesis / B cell activation / response to type II interferon / cell leading edge / MHC class I protein binding / host cell Golgi membrane / Synthesis of PIPs at the plasma membrane / intracellular copper ion homeostasis / protein targeting / side of membrane / COPI-mediated anterograde transport / clathrin-coated pit / regulation of calcium-mediated signaling / vesicle-mediated transport / viral life cycle / MHC class II antigen presentation / Neutrophil degranulation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / multivesicular body / sarcomere / small monomeric GTPase / trans-Golgi network membrane / negative regulation of cell migration / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / virion component / regulation of actin cytoskeleton organization / intracellular protein transport / response to virus / trans-Golgi network / cytoplasmic vesicle membrane / negative regulation of cell growth / cellular response to virus / SH3 domain binding / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / presynapse / heart development / ATPase binding / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / postsynaptic density / early endosome / neuron projection / apical plasma membrane / membrane raft / protein domain specific binding / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / innate immune response / signaling receptor binding / focal adhesion / GTPase activity / synapse / Neutrophil degranulation / GTP binding / apoptotic process Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.27 Å | |||||||||
![]() | Buffalo CZ / Morris KL / Hurley JH | |||||||||
Funding support | ![]()
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![]() | ![]() 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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.1 KB 12.1 KB | Display Display | ![]() |
Images | ![]() | 643.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d83MC ![]() 7454C ![]() 7455C ![]() 7456C ![]() 7457C ![]() 7458C ![]() 7563C ![]() 6cm9C ![]() 6criC ![]() 6d84C ![]() 6dffC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | AP-1:Arf1:Tetherin-Nef dileucine mutant dimer monomeric subunit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant
Entire | Name: Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant |
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Components |
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-Supramolecule #1: Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant
Supramolecule | Name: Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 230 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 8 Details: 20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV |
Details | AP-1:Arf1:Tetherin-Nef dileucine (LL164-165AA) mutant |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3712 pixel / Digitization - Dimensions - Height: 3840 pixel / Digitization - Frames/image: 3-28 / Number grids imaged: 1 / Number real images: 1989 / Average exposure time: 5.6 sec. / Average electron dose: 39.7 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 46849 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.6 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |