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Yorodumi- 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 | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN/PROTEIN TRANSPORT / nef / AP / HIV / trafficking / VIRAL PROTEIN / VIRAL PROTEIN-PROTEIN TRANSPORT complex | ||||||||||||
Function / homology | Function and homology information basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / symbiont-mediated suppression of host T-cell mediated immune response / AP-1 adaptor complex / trans-Golgi Network Vesicle Budding / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis ...basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / symbiont-mediated suppression of host T-cell mediated immune response / AP-1 adaptor complex / trans-Golgi Network Vesicle Budding / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis / platelet dense granule organization / regulation of receptor internalization / protein trimerization / 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 / Golgi to lysosome transport / Intra-Golgi traffic / 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 / GTP-dependent protein binding / suppression by virus of host autophagy / clathrin adaptor activity / MHC class II antigen presentation / melanosome organization / thioesterase binding / CD4 receptor binding / Nef Mediated CD4 Down-regulation / dendritic spine organization / determination of left/right symmetry / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / clathrin-coated vesicle / Lysosome Vesicle Biogenesis / clathrin binding / Golgi Associated Vesicle Biogenesis / positive regulation of natural killer cell mediated cytotoxicity / host cell Golgi membrane / cell leading edge / Synthesis of PIPs at the plasma membrane / kinesin binding / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / intracellular copper ion homeostasis / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / protein targeting / CD8 receptor binding / MHC class I protein binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / COPI-mediated anterograde transport / TAP binding / regulation of calcium-mediated signaling / clathrin-coated pit / protection from natural killer cell mediated cytotoxicity / vesicle-mediated transport / viral life cycle / 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 / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / detection of bacterium / Neutrophil degranulation / T cell receptor binding / sarcomere / small monomeric GTPase / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / virion component / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / cytoplasmic vesicle membrane / trans-Golgi network / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / T cell mediated cytotoxicity / recycling endosome / antigen processing and presentation of endogenous peptide antigen via MHC class I / cellular response to virus / small GTPase binding / positive regulation of T cell cytokine production / MHC class I protein complex / SH3 domain binding / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.6 Å | ||||||||||||
Authors | Hooy, R.M. / Hurley, J.H. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Sci Adv / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ux3.cif.gz | 350.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ux3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ux3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/7ux3 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/7ux3 | 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 (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Homo sapiens (human) / Gene: ARF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84077 #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.) Human immunodeficiency virus 1 / Gene: nef / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q90VU7 |
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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.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04439 |
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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.) Homo sapiens (human) / Gene: AP1B1, ADTB1, BAM22, CLAPB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q10567 |
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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.) Mus musculus (house mouse) / Gene: Ap1g1, Adtg, Clapg1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22892 |
#6: Protein | Mass: 48475.535 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 BL21(DE3) (bacteria) / References: UniProt: P35585 |
#7: Protein | Mass: 18305.273 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 BL21(DE3) (bacteria) / References: UniProt: Q96PC3 |
-Non-polymers , 2 types, 4 molecules
#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 |
-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. |
-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 FIELDBright-field microscopy / 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 |
-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 |
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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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