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Yorodumi- EMDB-7457: Structure of the HIV-Nef bound AP-1:Arf1 closed trimer monomeric ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7457 | |||||||||
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Title | Structure of the HIV-Nef bound AP-1:Arf1 closed trimer monomeric subunit | |||||||||
Map data | Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit | |||||||||
Sample |
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Function / homology | Function and homology information 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 / response to interferon-alpha / regulation of receptor internalization / melanosome assembly / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / 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 / positive regulation of leukocyte proliferation / 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 / azurophil granule membrane / clathrin binding / negative regulation of viral genome replication / Golgi Associated Vesicle Biogenesis / cell leading edge / MHC class I protein binding / response to type II interferon / B cell activation / Synthesis of PIPs at the plasma membrane / host cell Golgi membrane / intracellular copper ion homeostasis / trans-Golgi network membrane / 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 / multivesicular body / sarcomere / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Neutrophil degranulation / small monomeric GTPase / 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 / trans-Golgi network / response to virus / cytoplasmic vesicle membrane / cellular response to virus / negative regulation of cell growth / SH3 domain binding / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / presynapse / heart development / ATPase binding / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / early endosome / postsynaptic density / neuron projection / apical plasma membrane / membrane raft / protein domain specific binding / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / innate immune response / signaling receptor binding / focal adhesion / GTPase activity / Neutrophil degranulation / synapse / GTP binding / apoptotic process Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.73 Å | |||||||||
Authors | Morris KL / Buffalo CZ / 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7457.map.gz | 40.1 MB | EMDB map data format | |
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Header (meta data) | emd-7457-v30.xml emd-7457.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_7457.png | 672 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7457 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7457 | HTTPS FTP |
-Validation report
Summary document | emd_7457_validation.pdf.gz | 321.7 KB | Display | EMDB validaton report |
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Full document | emd_7457_full_validation.pdf.gz | 321.2 KB | Display | |
Data in XML | emd_7457_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7457 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7457 | HTTPS FTP |
-Related structure data
Related structure data | 6cm9MC 7453C 7454C 7455C 7456C 7458C 7563C 6criC 6d83C 6d84C 6dffC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10176 (Title: Single particle cryo-EM dataset of the flexible and variable oligomeric state complex AP-1:Arf1:tetherin-HIV-Nef Data size: 115.4 Data #1: Dose weighted particle stack of AP1:Arf1:tetherin-HIV-Nef [picked particles - multiframe - unprocessed]) EMPIAR-10177 (Title: Single particle cryo-EM dataset of the flexible and variable oligomeric state complex AP-1:Arf1:tetherin-HIV-Nef Data size: 34.0 Data #1: Dose weighted particle stack of AP1:Arf1:tetherin-HIV-Nef closed trimer [picked particles - multiframe - unprocessed]) EMPIAR-10178 (Title: Single particle cryo-EM dataset of the flexible and variable oligomeric state complex AP-1:Arf1:tetherin-HIV-Nef Data size: 10.1 Data #1: Dose weight particle stack of AP1:Arf1:tetherin-HIV-Nef closed trimer after monomeric subunit extraction using LocalRec [picked particles - multiframe - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7457.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Closed trimer assembly of AP-1:Arf1:Tetherin-Nef
Entire | Name: Closed trimer assembly of AP-1:Arf1:Tetherin-Nef |
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Components |
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-Supramolecule #1: Closed trimer assembly of AP-1:Arf1:Tetherin-Nef
Supramolecule | Name: Closed trimer assembly of AP-1:Arf1:Tetherin-Nef / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 230 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: 3-38 / Number grids imaged: 1 / Number real images: 2200 / Average exposure time: 9.5 sec. / Average electron dose: 62.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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: 2.0 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 |