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Yorodumi- EMDB-27188: Subtomogram average of AP-1, Arf1 and Nef complexes on narrow mem... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27188 | ||||||||||||
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Title | Subtomogram average of AP-1, Arf1 and Nef complexes on narrow membrane tubes centered on beta-Arf1 dimers | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | nef / AP / HIV / trafficking / VIRAL PROTEIN | ||||||||||||
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 / 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 / Lysosome Vesicle Biogenesis / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / clathrin binding / CD8-positive, alpha-beta T cell activation / Golgi Associated Vesicle Biogenesis / positive regulation of CD8-positive, alpha-beta T cell proliferation / Golgi medial cisterna / CD8 receptor binding / cell leading edge / MHC class I protein binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / Synthesis of PIPs at the plasma membrane / host cell Golgi 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 / trans-Golgi network membrane / beta-2-microglobulin binding / protein targeting / 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 / sarcomere / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Neutrophil degranulation / 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 / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / virion component / intracellular protein transport / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / cellular response to virus / MHC class I protein complex / SH3 domain binding / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / 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 / antibacterial humoral response / presynapse / heart development Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 20.0 Å | ||||||||||||
Authors | Hooy RM / Hurley JH | ||||||||||||
Funding support | United States, 3 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27188.map.gz | 3 MB | EMDB map data format | |
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Header (meta data) | emd-27188-v30.xml emd-27188.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27188_fsc.xml | 4.1 KB | Display | FSC data file |
Images | emd_27188.png | 63.9 KB | ||
Masks | emd_27188_msk_1.map | 5.4 MB | Mask map | |
Filedesc metadata | emd-27188.cif.gz | 5.2 KB | ||
Others | emd_27188_half_map_1.map.gz emd_27188_half_map_2.map.gz | 4.9 MB 4.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27188 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27188 | HTTPS FTP |
-Validation report
Summary document | emd_27188_validation.pdf.gz | 828.9 KB | Display | EMDB validaton report |
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Full document | emd_27188_full_validation.pdf.gz | 828.5 KB | Display | |
Data in XML | emd_27188_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | emd_27188_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27188 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27188 | HTTPS FTP |
-Related structure data
Related structure data | 8d9uMC 7ux3C 8d4cC 8d4dC 8d4eC 8d4fC 8d4gC 8d9rC 8d9sC 8d9tC 8d9vC 8d9wC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27188.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.2 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27188_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27188_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27188_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of AP-1, Arf1, Nef and MHC-I cytosolic tail on a tubulate...
Entire | Name: Complex of AP-1, Arf1, Nef and MHC-I cytosolic tail on a tubulated lipid bilayer |
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Components |
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-Supramolecule #1: Complex of AP-1, Arf1, Nef and MHC-I cytosolic tail on a tubulate...
Supramolecule | Name: Complex of AP-1, Arf1, Nef and MHC-I cytosolic tail on a tubulated lipid bilayer type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 Details: Subtomogram average encompasses multiple AP-1 dimers |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: AP-1 heterotetramer
Supramolecule | Name: AP-1 heterotetramer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4-#5, #7-#8 Details: All four subunits are co-expressed from the same plasmid. Assembly occurs in situ during expression. |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | |||||||||||||||
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Buffer | pH: 7.2 Component:
Details: HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments. | |||||||||||||||
Grid | Model: EMS Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 50 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV 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
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 25 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Average exposure time: 3.0 sec. / Average electron dose: 3.0 e/Å2 Details: Tilt images were collected in movie-mode. Each movie/tilt consisted of 3-4 frames each |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8d9u: |