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Yorodumi- EMDB-7563: Structure of the HIV-Nef tetherin cargo bound AP-1:Arf1 stable cl... -
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-Basic information
Entry | Database: EMDB / ID: EMD-7563 | |||||||||
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Title | Structure of the HIV-Nef tetherin cargo bound AP-1:Arf1 stable closed trimer | |||||||||
Map data | HIV-Nef tetherin cargo bound AP-1:Arf1 stable closed trimer | |||||||||
Sample |
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Keywords | AP / HIV / Nef / trafficking / VIRAL PROTEIN / PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / basolateral protein secretion / negative regulation of CD4 production / perturbation by virus of host immune response / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex ...negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / basolateral protein secretion / negative regulation of CD4 production / perturbation by virus of host immune response / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / protein trimerization / platelet dense granule organization / Glycosphingolipid transport / response to interferon-alpha / regulation of receptor internalization / melanosome assembly / metalloendopeptidase inhibitor activity / Intra-Golgi traffic / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / 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 / positive regulation of leukocyte proliferation / 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 / azurophil granule membrane / Lysosome Vesicle Biogenesis / negative regulation of viral genome replication / clathrin binding / Golgi Associated Vesicle Biogenesis / cell leading edge / MHC class I protein binding / response to type II interferon / B cell activation / Synthesis of PIPs at the plasma membrane / host cell Golgi membrane / intracellular copper ion homeostasis / protein targeting / COPI-mediated anterograde transport / side of membrane / 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 / multivesicular body / Neutrophil degranulation / sarcomere / small monomeric GTPase / kidney development / trans-Golgi network membrane / negative regulation of cell migration / Nef mediated downregulation of MHC class I complex cell surface expression / regulation of actin cytoskeleton organization / intracellular protein transport / virion component / trans-Golgi network / response to virus / cytoplasmic vesicle membrane / negative regulation of cell growth / cellular response to virus / SH3 domain binding / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / heart development / presynapse / ATPase binding / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / postsynaptic density / early endosome / neuron projection / membrane raft / apical plasma membrane / protein domain specific binding / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / innate immune response / signaling receptor binding / focal adhesion / GTPase activity / Neutrophil degranulation / synapse / GTP binding / apoptotic process Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human immunodeficiency virus 1 / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||
Authors | Morris KL / Buffalo CZ / Hurley JH | |||||||||
Funding support | United States, 1 items
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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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7563.map.gz | 201.5 MB | EMDB map data format | |
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Header (meta data) | emd-7563-v30.xml emd-7563.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7563_fsc.xml | 13.8 KB | Display | FSC data file |
Images | emd_7563.png | 194.1 KB | ||
Filedesc metadata | emd-7563.cif.gz | 7.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7563 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7563 | HTTPS FTP |
-Validation report
Summary document | emd_7563_validation.pdf.gz | 389.5 KB | Display | EMDB validaton report |
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Full document | emd_7563_full_validation.pdf.gz | 389.1 KB | Display | |
Data in XML | emd_7563_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | emd_7563_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7563 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7563 | HTTPS FTP |
-Related structure data
Related structure data | 6criMC 7453C 7454C 7455C 7456C 7457C 7458C 6cm9C 6d83C 6d84C 6dffC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7563.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HIV-Nef tetherin cargo bound AP-1:Arf1 stable closed trimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed...
Entire | Name: Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer |
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Components |
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-Supramolecule #1: Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed...
Supramolecule | Name: Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 700 KDa |
-Macromolecule #1: Bone marrow stromal antigen 2, Protein Nef chimera
Macromolecule | Name: Bone marrow stromal antigen 2, Protein Nef chimera / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Human immunodeficiency virus 1 |
Molecular weight | Theoretical: 29.964326 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSYYHHHHHH DYDIPTTENL YFQGAMGSAS TSYDYCRVPM EDGDKRCKGS DEASEGSGMG GKWSKSSVIG WPAVRERMRR AEPAADGVG AVSRDLEKHG AITSSNTAAN NAACAWLEAQ EEEEVGFPVT PQVPLRPMTY KAAVDLSHFL KEKGGLEGLI H SQRRQDIL ...String: MSYYHHHHHH DYDIPTTENL YFQGAMGSAS TSYDYCRVPM EDGDKRCKGS DEASEGSGMG GKWSKSSVIG WPAVRERMRR AEPAADGVG AVSRDLEKHG AITSSNTAAN NAACAWLEAQ EEEEVGFPVT PQVPLRPMTY KAAVDLSHFL KEKGGLEGLI H SQRRQDIL DLWIYHTQGY FPDWQNYTPG PGVRYPLTFG WCYKLVPVEP DKVEEANKGE NTSLLHPVSL HGMDDPEREV LE WRFDSRL AFHHVARELH PEYFKNC UniProtKB: Bone marrow stromal antigen 2, Protein Nef |
-Macromolecule #2: AP-1 complex subunit beta-1
Macromolecule | Name: AP-1 complex subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 64.458656 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EIFELKAELN SDKKEKKKEA VKKVIASMTV GKDVSALFPD VVNCMQTDNL ELKKLVYLYL MNYAKSQPDM AIMAVNTFVK DCEDPNPLI RALAVRTMGC IRVDKITEYL CEPLRKCLKD EDPYVRKTAA VCVAKLHDIN AQLVEDQGFL DTLKDLISDS N PMVVANAV ...String: EIFELKAELN SDKKEKKKEA VKKVIASMTV GKDVSALFPD VVNCMQTDNL ELKKLVYLYL MNYAKSQPDM AIMAVNTFVK DCEDPNPLI RALAVRTMGC IRVDKITEYL CEPLRKCLKD EDPYVRKTAA VCVAKLHDIN AQLVEDQGFL DTLKDLISDS N PMVVANAV AALSEIAESH PSSNLLDLNP QSINKLLTAL NECTEWGQIF ILDCLANYMP KDDREAQSIC ERVTPRLSHA NS AVVLSAV KVLMKFMEML SKDLDYYGTL LKKLAPPLVT LLSAEPELQY VALRNINLIV QKRPEILKHE MKVFFVKYND PIY VKLEKL DIMIRLASQA NIAQVLAELR EYATEVDVDF VRKAVRAIGR CAIKVEQSAE RCVSTLLDLI QTKVNYVVQE AIVV IKDIF RKYPNKYESV IATLCENLDS LDEPEARAAM IWIVGEYAER IDNADELLES FLEGFHDKST QVQLQLLTAI VKLFL KKPT ETQELVQQVL SLATQDSDNP DLRDRGYIYW RLLSTDPVAA KEVVLAEKPL ISEETDLIEP TLLDELICYI GTLASV YHK PPSAFVE UniProtKB: AP-1 complex subunit beta-1 |
-Macromolecule #3: ADP-ribosylation factor 1
Macromolecule | Name: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 18.9366 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EMRILMVGLD AAGKTTILYK LKLGEIVTTI PTIGFNVETV EYKNISFTVW DVGGLDKIRP LWRHYFQNTQ GLIFVVDSND RERVNEARE ELMRMLAEDE LRDAVLLVFA NKQDLPNAMN AAEITDKLGL HSLRHRNWYI QATCATSGDG LYEGLDWLSN Q LRNQK UniProtKB: ADP-ribosylation factor 1 |
-Macromolecule #4: AP-1 complex subunit gamma-1
Macromolecule | Name: AP-1 complex subunit gamma-1 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 66.401055 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PIRLRELIRT IRTARTQAEE REMIQKECAA IRSSFREEDN TYRCRNVAKL LYMHMLGYPA HFGQLECLKL IASQKFTDKR IGYLGAMLL LDERQDVHLL MTNCIKNDLN HSTQFVQGLA LCTLGCMGSS EMCRDLAGEV EKLLKTSNSY LRKKAALCAV H VIRKVPEL ...String: PIRLRELIRT IRTARTQAEE REMIQKECAA IRSSFREEDN TYRCRNVAKL LYMHMLGYPA HFGQLECLKL IASQKFTDKR IGYLGAMLL LDERQDVHLL MTNCIKNDLN HSTQFVQGLA LCTLGCMGSS EMCRDLAGEV EKLLKTSNSY LRKKAALCAV H VIRKVPEL MEMFLPATKN LLNEKNHGVL HTSVVLLTEM CERSPDMLAH FRKLVPQLVR ILKNLIMSGY SPEHDVSGIS DP FLQVRIL RLLRILGRND DDSSEAMNDI LAQVATNTET SKNVGNAILY ETVLTIMDIK SESGLRVLAI NILGRFLLNN DKN IRYVAL TSLLKTVQTD HNAVQRHRST IVDCLKDLDV SIKRRAMELS FALVNGNNIR GMMKELLYFL DSCEPEFKAD CASG IFLAA EKYAPSKRWH IDTIMRVLTT AGSYVRDDAV PNLIQLITNS VEMHAYTVQR LYKAILGDYS QQPLVQVAAW CIGEY GDLL VSGQCEEEEP IQVTEDEVLD ILESVLISNM STSVTRGYAL TAIMKLSTRF TCTVNRIKKV VSIYGSSIDV ELQQRA VEY NALFKKYDHM RSALLERMPV ME UniProtKB: AP-1 complex subunit gamma-1 |
-Macromolecule #5: AP-1 complex subunit mu-1
Macromolecule | Name: AP-1 complex subunit mu-1 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 48.475535 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SASAVYVLDL KGKVLICRNY RGDVDMSEVE HFMPILMEKE EEGMLSPILA HGGVRFMWIK HNNLYLVATS KKNACVSLVF SFLYKVVQV FSEYFKELEE ESIRDNFVII YELLDELMDF GYPQTTDSKI LQEYITQEGH KLETGAPRPP ATVTNAVSWR S EGIKYRKN ...String: SASAVYVLDL KGKVLICRNY RGDVDMSEVE HFMPILMEKE EEGMLSPILA HGGVRFMWIK HNNLYLVATS KKNACVSLVF SFLYKVVQV FSEYFKELEE ESIRDNFVII YELLDELMDF GYPQTTDSKI LQEYITQEGH KLETGAPRPP ATVTNAVSWR S EGIKYRKN EVFLDVIEAV NLLVSANGNV LRSEIVGSIK MRVFLSGMPE LRLGLNDKVL FDNTGRGKSK SVELEDVKFH QC VRLSRFE NDRTISFIPP DGEFELMSYR LNTHVKPLIW IESVIEKHSH SRIEYMVKAK SQFKRRSTAN NVEIHIPVPN DAD SPKFKT TVGSVKWVPE NSEIVWSVKS FPGGKEYLMR AHFGLPSVEA EDKEGKPPIS VKFEIPYFTT SGIQVRYLKI IEKS GYQAL PWVRYITQNG DYQLRTQ UniProtKB: AP-1 complex subunit mu-1 |
-Macromolecule #6: AP-1 complex subunit sigma-3
Macromolecule | Name: AP-1 complex subunit sigma-3 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 16.99885 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIHFILLFSR QGKLRLQKWY ITLPDKERKK ITREIVQIIL SRGHRTSSFV DWKELKLVYK RYASLYFCCA IENQDNELLT LEIVHRYVE LLDKYFGNVC ELDIIFNFEK AYFILDEFII GGEIQETSKK IAVKAIEDSD MLQ UniProtKB: AP-1 complex subunit sigma-3 |
-Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 6 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #8: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.07 mg/mL |
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Buffer | pH: 8 Details: 20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP |
Grid | Pretreatment - Type: PLASMA CLEANING / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 296 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 62.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 425 / Target criteria: Correlation coefficient |
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Output model | PDB-6cri: |