|Entry||Database: EMDB / ID: EMD-7455|
|Title||Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer|
|Sample||Monomer of AP-1:Arf1:Tetherin-Nef|
|Function / homology|
Function and homology information
negative regulation of intracellular transport of viral material / negative regulation of plasmacytoid dendritic cell cytokine production / phospholipase D activator activity / mitotic cleavage furrow ingression / Golgi to transport vesicle transport / regulation of phospholipid metabolic process / positive regulation of late endosome to lysosome transport / lysosomal membrane organization / synaptic vesicle budding / suppression by symbiont of host T-cell mediated immune response ...negative regulation of intracellular transport of viral material / negative regulation of plasmacytoid dendritic cell cytokine production / phospholipase D activator activity / mitotic cleavage furrow ingression / Golgi to transport vesicle transport / regulation of phospholipid metabolic process / positive regulation of late endosome to lysosome transport / lysosomal membrane organization / synaptic vesicle budding / suppression by symbiont of host T-cell mediated immune response / negative regulation of CD4 biosynthetic process / positive regulation of leukocyte proliferation / AP-1 adaptor complex / regulation of Arp2/3 complex-mediated actin nucleation / clathrin adaptor complex / positive regulation of natural killer cell degranulation / positive regulation of ER to Golgi vesicle-mediated transport / endosome to melanosome transport / Golgi to lysosome transport / response to interferon-beta / very-low-density lipoprotein particle assembly / melanosome organization / regulation of receptor internalization / suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I / response to interferon-alpha / COPI-coated vesicle / postsynaptic actin cytoskeleton organization / suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host adaptive immune response / metalloendopeptidase inhibitor activity / membrane coat / suppression by virus of host autophagy / positive regulation of calcium ion-dependent exocytosis / GTP-dependent protein binding / positive regulation of natural killer cell mediated cytotoxicity / long-term synaptic depression / CD4 receptor binding / determination of left/right symmetry / dendritic spine organization / thioesterase binding / regulation of calcium-mediated signaling / peroxisomal membrane / host cell Golgi membrane / azurophil granule membrane / clathrin binding / positive regulation of dendritic spine development / clathrin-coated vesicle / kinesin binding / MHC class I protein binding / positive regulation of endocytosis / B cell activation / response to interferon-gamma / cell leading edge / positive regulation of sodium ion transmembrane transport / negative regulation of viral genome replication / phosphatidylinositol biosynthetic process / cellular copper ion homeostasis / protein targeting / trans-Golgi network membrane / clathrin-coated pit / Rab GTPase binding / cellular response to virus / antigen processing and presentation of exogenous peptide antigen via MHC class II / clathrin-coated vesicle membrane / regulation of actin cytoskeleton organization / negative regulation of cell migration / anchored component of membrane / sarcomere / positive regulation of protein secretion / actin filament organization / vesicle-mediated transport / multivesicular body / microtubule cytoskeleton organization / collagen binding / interleukin-12-mediated signaling pathway / response to virus / microtubule cytoskeleton / GDP binding / type I interferon signaling pathway / recycling endosome / intracellular protein transport / virion / cytoplasmic vesicle membrane / trans-Golgi network / regulation of defense response to virus by virus / viral life cycle / SH3 domain binding / negative regulation of cell growth / lysosomal membrane / defense response to virus / late endosome / apical plasma membrane / heart development / positive regulation of I-kappaB kinase/NF-kappaB signaling / ATPase binding / protein C-terminus binding / postsynaptic density / GTPase activity / neuron projection / Golgi membrane
Clathrin adaptor, appendage, Ig-like subdomain superfamily / AP complex, mu/sigma subunit / Beta-adaptin appendage, C-terminal subdomain / Clathrin adaptor, mu subunit / HIV negative factor Nef / Clathrin adaptor complex, small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Small GTP-binding protein domain / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / TBP domain superfamily ...Clathrin adaptor, appendage, Ig-like subdomain superfamily / AP complex, mu/sigma subunit / Beta-adaptin appendage, C-terminal subdomain / Clathrin adaptor, mu subunit / HIV negative factor Nef / Clathrin adaptor complex, small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Small GTP-binding protein domain / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / TBP domain superfamily / Adaptor protein complex, sigma subunit / Armadillo-like helical / Adaptor protein complex AP-1, gamma subunit / Clathrin adaptor, mu subunit, conserved site / Small GTPase superfamily, ARF/SAR type / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / AP-1/2/4 complex subunit beta / Armadillo / Gamma-adaptin ear (GAE) domain / Bone marrow stromal antigen 2 / AP complex subunit beta / P-loop containing nucleoside triphosphate hydrolase / HIV-1 Nef protein, anchor domain superfamily / Coatomer/calthrin adaptor appendage, C-terminal subdomain / HIV-1 Nef protein, core domain superfamily / Mu homology domain / Longin-like domain superfamily / AP-2 complex subunit mu, C-terminal superfamily / Armadillo-type fold
AP-1 complex subunit gamma-1 / AP-1 complex subunit mu-1 / ADP-ribosylation factor 1 / AP-1 complex subunit beta-1 / Bone marrow stromal antigen 2 / Protein Nef / AP-1 complex subunit sigma-3
|Biological species||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.9 Å|
|Authors||Morris KL / Buffalo CZ / Hurley JH|
|Citation||Journal: Cell / Year: 2018|
Title: HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation.
Authors: Kyle L Morris / Cosmo Z Buffalo / Christina M Stürzel / Elena Heusinger / Frank Kirchhoff / Xuefeng Ren / James H Hurley /
Abstract: The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 Å cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, ...The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 Å cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, HIV-1 Nef, and the cytosolic tail of the restriction factor tetherin suggested a mechanism for inactivating tetherin by Golgi retention. The 4.3 Å structure of a mutant Nef-induced dimer of AP-1 showed how the closed trimer is regulated by the dileucine loop of Nef. HDX-MS and mutational analysis were used to show how cargo dynamics leads to alternative Arf1 trimerization, directing Nef targets to be either retained at the trans-Golgi or sorted to lysosomes. Phosphorylation of the NL4-3 M-Nef was shown to regulate AP-1 trimerization, explaining how O-Nefs lacking this phosphosite counteract tetherin but most M-Nefs do not. These observations show how the higher-order organization of a vesicular coat can be allosterically modulated to direct cargoes to distinct fates.
|Validation Report||PDB-ID: 6dff|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_7455.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.067 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Monomer of AP-1:Arf1:Tetherin-Nef
|Entire||Name: Monomer of AP-1:Arf1:Tetherin-Nef / Number of components: 1|
-Component #1: protein, Monomer of AP-1:Arf1:Tetherin-Nef
|Protein||Name: Monomer of AP-1:Arf1:Tetherin-Nef / Recombinant expression: No|
|Mass||Theoretical: 700 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.7 mg/mL|
Buffer solution: 20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 294 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 62.4 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 22500.0 X (nominal), 46849.0 X (calibrated) / Cs: 2.6 mm / Imaging mode: BRIGHT FIELD / Defocus: 750.0 - 2000.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 2200|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 53123|
|3D reconstruction||Software: RELION / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi