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Yorodumi- EMDB-27186: Beta-Arf1 homodimeric interface within AP-1 lattice on narrow mem... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27186 | ||||||||||||
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Title | Beta-Arf1 homodimeric interface within AP-1 lattice on narrow membrane tubes | ||||||||||||
Map data | |||||||||||||
Sample |
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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 / 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 / symbiont-mediated suppression of host apoptosis / Synthesis of PIPs at the Golgi membrane / Golgi Associated Vesicle Biogenesis / 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 / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / 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 / MHC class I protein binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / host cell Golgi membrane / 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 / 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 / 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 / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / virion component / 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 / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / trans-Golgi network / 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 / Interferon alpha/beta signaling / positive regulation of type II interferon production / E3 ubiquitin ligases ubiquitinate target proteins / heart development / T cell receptor signaling pathway / ER-Phagosome pathway Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.3 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_27186.map.gz | 5.2 MB | EMDB map data format | |
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Header (meta data) | emd-27186-v30.xml emd-27186.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27186_fsc.xml | 4.7 KB | Display | FSC data file |
Images | emd_27186.png | 35.5 KB | ||
Masks | emd_27186_msk_1.map | 8 MB | Mask map | |
Others | emd_27186_half_map_1.map.gz emd_27186_half_map_2.map.gz | 7.3 MB 7.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27186 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27186 | HTTPS FTP |
-Validation report
Summary document | emd_27186_validation.pdf.gz | 626.1 KB | Display | EMDB validaton report |
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Full document | emd_27186_full_validation.pdf.gz | 625.7 KB | Display | |
Data in XML | emd_27186_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | emd_27186_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27186 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27186 | HTTPS FTP |
-Related structure data
Related structure data | 8d9wMC 7ux3C 8d4cC 8d4dC 8d4eC 8d4fC 8d4gC 8d9rC 8d9sC 8d9tC 8d9uC 8d9vC 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_27186.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 2.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27186_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27186_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27186_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Assembly of AP-1, Arf1 and Nef complexes on narrow membrane tubes
Entire | Name: Assembly of AP-1, Arf1 and Nef complexes on narrow membrane tubes |
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Components |
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-Supramolecule #1: Assembly of AP-1, Arf1 and Nef complexes on narrow membrane tubes
Supramolecule | Name: Assembly of AP-1, Arf1 and Nef complexes on narrow membrane tubes type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 Details: Subtomogram average of beta-Arf1 homodimeric interface within AP-1 lattice on narrow membrane tubes |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: AP-1 heterotetramer
Supramolecule | Name: AP-1 heterotetramer / type: complex / Chimera: Yes / 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) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-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: 50.0 nm | |||||||||||||||
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-8d9w: |