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- PDB-7ux3: Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide i... -
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Basic information
Entry | Database: PDB / ID: 7ux3 | ||||||||||||
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Title | Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes | ||||||||||||
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![]() | VIRAL PROTEIN/PROTEIN TRANSPORT / nef / AP / HIV / trafficking / VIRAL PROTEIN / VIRAL PROTEIN-PROTEIN TRANSPORT complex | ||||||||||||
Function / homology | ![]() 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 ...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 / 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 / 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 / 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 / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Lysosome Vesicle Biogenesis / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / clathrin binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / Golgi Associated Vesicle Biogenesis / CD8 receptor binding / cell leading edge / antigen processing and presentation of exogenous peptide antigen via MHC class I / MHC class I protein binding / endoplasmic reticulum exit site / host cell Golgi membrane / Synthesis of PIPs at the plasma membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / intracellular copper ion homeostasis / protein targeting / beta-2-microglobulin binding / COPI-mediated anterograde transport / T cell receptor binding / detection of bacterium / 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 / sarcomere / small monomeric GTPase / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / kidney development / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / MHC class I peptide loading complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / cellular response to virus / MHC class I protein complex / SH3 domain binding / virion component / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of type II interferon production / peptide antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / Interferon alpha/beta signaling / E3 ubiquitin ligases ubiquitinate target proteins / early endosome membrane / ATPase binding / presynapse Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.6 Å | ||||||||||||
![]() | Hooy, R.M. / Hurley, J.H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat. Authors: Richard M Hooy / Yuichiro Iwamoto / Dan A Tudorica / Xuefeng Ren / James H Hurley / ![]() 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. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 356.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 26853MC ![]() 8d4cC ![]() 8d4dC ![]() 8d4eC ![]() 8d4fC ![]() 8d4gC ![]() 8d9rC ![]() 8d9sC ![]() 8d9tC ![]() 8d9uC ![]() 8d9vC ![]() 8d9wC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 4 molecules CHNL
#1: Protein | Mass: 20800.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: glycine at position 2 is myristoylated - experimentally validated by mass spectrometry Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 24364.404 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: dileucine loop from adjacent protomer / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Protein/peptide , 1 types, 1 molecules Y
#3: Protein/peptide | Mass: 4542.884 Da / Num. of mol.: 1 / Mutation: T345S, S349G, G355S, C363A Source method: isolated from a genetically manipulated source Details: C-terminal fragment / Source: (gene. exp.) ![]() ![]() ![]() |
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-AP-1 complex subunit ... , 4 types, 4 molecules BGMS
#4: Protein | Mass: 104605.266 Da / Num. of mol.: 1 / Mutation: K359R,E476K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#5: Protein | Mass: 68062.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#6: Protein | Mass: 48475.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#7: Protein | Mass: 18305.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 2 types, 4 molecules ![](data/chem/img/GTP.gif)
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#8: Chemical | #9: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
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Sample preparation
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Buffer solution | pH: 7.2 Details: HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments. | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: EMS Lacey Carbon | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K Details: 60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted. |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 42000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 3 e/Å2 / Avg electron dose per subtomogram: 123 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 Details: Tilt images were collected in movie-mode. Each movie/tilt consisted of 3-4 frames each |
EM imaging optics | Energyfilter slit width: 25 eV |
Image scans | Width: 5760 / Height: 4092 |
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Processing
Software |
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EM software |
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Image processing | Details: The images were gain-normalized | ||||||||||||||||||||||||||||||||
CTF correction | Details: CTF was estimated on a per-tilt basis in IMOD (4.11) using CTFPLOTTER. The results were used as input to NOVACTF during 3DCTF correction. Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 9.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16422 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
EM volume selection | Details: Tubes were annotated by tracing the center of the tube in Dynamo and recording the average apparent diameter. Initial subtomogram positions were picked using uniform radial and axial sampling. Num. of tomograms: 31 / Num. of volumes extracted: 61864 / Reference model: Reference-free | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.79 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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