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Yorodumi- PDB-8d4c: beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d4c | ||||||||||||
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Title | beta-Arf1 mediated dimeric assembly of AP-1, Arf1, Nef complex within lattice on MHC-I lipopeptide incorporated narrow membrane tubes | ||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / nef / AP / trafficking | ||||||||||||
Function / homology | Function and homology information Glycosphingolipid transport / basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / AP-1 adaptor complex / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / Lysosome Vesicle Biogenesis / platelet dense granule organization ...Glycosphingolipid transport / basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / AP-1 adaptor complex / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / Lysosome Vesicle Biogenesis / platelet dense granule organization / regulation of receptor internalization / protein trimerization / melanosome assembly / symbiont-mediated suppression of host apoptosis / 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 / 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 / suppression by virus of host autophagy / clathrin adaptor activity / MHC class II antigen presentation / thioesterase binding / CD4 receptor binding / Nef Mediated CD4 Down-regulation / 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 / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / clathrin binding / Golgi medial cisterna / Golgi Associated Vesicle Biogenesis / 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 / CD8 receptor binding / host cell Golgi membrane / cell leading edge / antigen processing and presentation of exogenous peptide antigen via MHC class I / MHC class I protein binding / endoplasmic reticulum exit site / 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 / intracellular copper ion homeostasis / protection from natural killer cell mediated cytotoxicity / protein targeting / beta-2-microglobulin binding / COPI-mediated anterograde transport / detection of bacterium / T cell receptor binding / clathrin-coated pit / vesicle-mediated transport / regulation of calcium-mediated signaling / viral life cycle / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Neutrophil degranulation / sarcomere / small monomeric GTPase / 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 / 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 / trans-Golgi network / cytoplasmic vesicle membrane / 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 / 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 / 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 / Interferon gamma signaling / positive regulation of type II interferon production / Interferon alpha/beta signaling / E3 ubiquitin ligases ubiquitinate target proteins / heart development / T cell receptor signaling pathway / ER-Phagosome pathway Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Human immunodeficiency virus 1 Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.3 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 | 8d4c.cif.gz | 678.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d4c.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8d4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/8d4c ftp://data.pdbj.org/pub/pdb/validation_reports/d4/8d4c | HTTPS FTP |
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-Related structure data
Related structure data | 27181MC 7ux3C 8d4dC 8d4eC 8d4fC 8d4gC 8d9rC 8d9sC 8d9tC 8d9uC 8d9vC 8d9wC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 8 molecules CHDFNLKI
#1: Protein | Mass: 20590.547 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N-terminal myristoylation / Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84077 #2: Protein | Mass: 24154.049 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N-terminal myristoylation / 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, 2 molecules YP
#3: Protein/peptide | Mass: 4139.429 Da / Num. of mol.: 2 / Mutation: T345S, S349G, G355S, C363A Source method: isolated from a genetically manipulated source Details: Conjugated to lipid maleimide via N-terminal cysteine 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, 8 molecules BAGEMJSO
#4: Protein | Mass: 104605.266 Da / Num. of mol.: 2 / 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 #5: Protein | Mass: 68062.891 Da / Num. of mol.: 2 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: 48606.730 Da / Num. of mol.: 2 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.: 2 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 |
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-Non-polymers , 2 types, 8 molecules
#8: Chemical | ChemComp-GTP / #9: Chemical | ChemComp-MG / |
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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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Source (recombinant) |
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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 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: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7004 / 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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