+Open data
-Basic information
Entry | Database: PDB / ID: 6dff | ||||||
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Title | Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / AP / HIV / Nef / trafficking / VIRAL PROTEIN / PROTEIN TRANSPORT | ||||||
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 / 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 / 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 / virion component / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / ATPase binding / presynapse / heart development / 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 / focal adhesion / signaling receptor binding / GTPase activity / synapse / Neutrophil degranulation / GTP binding / protein kinase binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Morris, K.L. / Buffalo, C.Z. / Ren, X. / Hurley, J.H. | ||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6dff.cif.gz | 389.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dff.ent.gz | 304.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dff_validation.pdf.gz | 903.4 KB | Display | wwPDB validaton report |
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Full document | 6dff_full_validation.pdf.gz | 916.3 KB | Display | |
Data in XML | 6dff_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 6dff_validation.cif.gz | 86 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/6dff ftp://data.pdbj.org/pub/pdb/validation_reports/df/6dff | HTTPS FTP |
-Related structure data
Related structure data | 7455MC 7453C 7454C 7456C 7457C 7458C 7563C 6cm9C 6criC 6d83C 6d84C M: map data used to model this data C: citing same article (ref.) |
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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
-Assembly
Deposited unit |
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-Components
-Protein , 2 types, 4 molecules LTCH
#1: Protein | Mass: 29964.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Human immunodeficiency virus 1 Gene: BST2, nef / Production host: Escherichia coli (E. coli) / References: UniProt: Q10589, UniProt: Q90VU7 #3: Protein | Mass: 22314.250 Da / Num. of mol.: 2 / Mutation: Q71L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P84077 |
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-AP-1 complex subunit ... , 4 types, 4 molecules BGMS
#2: Protein | Mass: 66152.547 Da / Num. of mol.: 1 / Mutation: K359R, E476K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AP1B1, ADTB1, BAM22, CLAPB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q10567 |
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#4: Protein | Mass: 68194.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1g1, Adtg, Clapg1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22892 |
#5: Protein | Mass: 48606.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1m1, Cltnm / Production host: Escherichia coli (E. coli) / References: UniProt: P35585 |
#6: Protein | Mass: 18321.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AP1S3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96PC3 |
-Non-polymers , 2 types, 4 molecules
#7: Chemical | #8: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 294 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 46849 X / Nominal defocus max: 2000 nm / Nominal defocus min: 750 nm / Cs: 2.6 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 9.5 sec. / Electron dose: 62.4 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2200 |
Image scans | Width: 3712 / Height: 3840 / Movie frames/image: 38 / Used frames/image: 3-28 |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 252212 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53123 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient / Details: Phenix real space refine | ||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refine LS restraints |
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