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- EMDB-7563: Structure of the HIV-Nef tetherin cargo bound AP-1:Arf1 stable cl... -

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Entry
Database: EMDB / ID: EMD-7563
TitleStructure of the HIV-Nef tetherin cargo bound AP-1:Arf1 stable closed trimer
Map dataHIV-Nef tetherin cargo bound AP-1:Arf1 stable closed trimer
Sample
  • Complex: Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer
    • Protein or peptide: Bone marrow stromal antigen 2, Protein Nef chimera
    • Protein or peptide: AP-1 complex subunit beta-1AP-1 transcription factor
    • Protein or peptide: ADP-ribosylation factor 1ARF1
    • Protein or peptide: AP-1 complex subunit gamma-1AP-1 transcription factor
    • Protein or peptide: AP-1 complex subunit mu-1AP-1 transcription factor
    • Protein or peptide: AP-1 complex subunit sigma-3AP-1 transcription factor
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
KeywordsAP / 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 / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / symbiont-mediated suppression of host T-cell mediated immune response / AP-1 adaptor complex / trans-Golgi Network Vesicle Budding ...negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / symbiont-mediated suppression of host T-cell mediated immune response / AP-1 adaptor complex / trans-Golgi Network Vesicle Budding / endosome to melanosome transport / positive regulation of natural killer cell degranulation / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization / regulation of receptor internalization / melanosome assembly / response to interferon-alpha / regulation of Arp2/3 complex-mediated actin nucleation / Golgi to lysosome transport / Intra-Golgi traffic / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / Golgi to vacuole transport / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / metalloendopeptidase inhibitor activity / Golgi Associated Vesicle Biogenesis / Synthesis of PIPs at the Golgi membrane / melanosome organization / GTP-dependent protein binding / suppression by virus of host autophagy / clathrin adaptor activity / MHC class II antigen presentation / positive regulation of leukocyte proliferation / thioesterase binding / CD4 receptor binding / Nef Mediated CD4 Down-regulation / dendritic spine organization / determination of left/right symmetry / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / clathrin-coated vesicle / azurophil granule membrane / Lysosome Vesicle Biogenesis / clathrin binding / Golgi Associated Vesicle Biogenesis / negative regulation of viral genome replication / B cell activation / positive regulation of natural killer cell mediated cytotoxicity / response to type II interferon / host cell Golgi membrane / cell leading edge / Synthesis of PIPs at the plasma membrane / kinesin binding / intracellular copper ion homeostasis / protein targeting / MHC class I protein binding / side of membrane / COPI-mediated anterograde transport / regulation of calcium-mediated signaling / clathrin-coated pit / vesicle-mediated transport / viral life cycle / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Neutrophil degranulation / multivesicular body / sarcomere / small monomeric GTPase / negative regulation of cell migration / trans-Golgi network membrane / kidney development / Nef mediated downregulation of MHC class I complex cell surface expression / virion component / regulation of actin cytoskeleton organization / intracellular protein transport / response to virus / trans-Golgi network / cytoplasmic vesicle membrane / negative regulation of cell growth / recycling endosome / small GTPase binding / cellular response to virus / SH3 domain binding / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / heart development / 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 / lysosomal membrane / protein domain specific binding / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response
Similarity search - Function
Bone marrow stromal antigen 2 / Bone marrow stromal antigen 2 / AP-1 complex subunit sigma / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / HIV-1 Nef protein, anchor domain superfamily / ADP-ribosylation factor 1-5 / Adaptor protein complex, sigma subunit / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain ...Bone marrow stromal antigen 2 / Bone marrow stromal antigen 2 / AP-1 complex subunit sigma / Adaptor protein complex AP-1, gamma subunit / Gamma-adaptin ear (GAE) domain / Gamma-adaptin ear (GAE) domain profile. / HIV-1 Nef protein, anchor domain superfamily / ADP-ribosylation factor 1-5 / Adaptor protein complex, sigma subunit / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / small GTPase Arf family profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Longin-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
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
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsMorris KL / Buffalo CZ / Hurley JH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI 120691 United States
CitationJournal: 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
DepositionMar 18, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseAug 1, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0149
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0149
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cri
  • Surface level: 0.0149
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7563.png

Downloads & links

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Map

FileDownload / File: emd_7563.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-Nef tetherin cargo bound AP-1:Arf1 stable closed trimer
Voxel sizeX=Y=Z: 1.067 Å
Density
Contour LevelBy AUTHOR: 0.0149 / Movie #1: 0.0149
Minimum - Maximum-0.017942984 - 0.058546383
Average (Standard dev.)0.0003145799 (±0.002489533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 409.72803 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z409.728409.728409.728
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0180.0590.000

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Supplemental data

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Sample components

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Entire : Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed...

EntireName: Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer
Components
  • Complex: Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer
    • Protein or peptide: Bone marrow stromal antigen 2, Protein Nef chimera
    • Protein or peptide: AP-1 complex subunit beta-1AP-1 transcription factor
    • Protein or peptide: ADP-ribosylation factor 1ARF1
    • Protein or peptide: AP-1 complex subunit gamma-1AP-1 transcription factor
    • Protein or peptide: AP-1 complex subunit mu-1AP-1 transcription factor
    • Protein or peptide: AP-1 complex subunit sigma-3AP-1 transcription factor
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed...

SupramoleculeName: Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: Bone marrow stromal antigen 2, Protein Nef chimera

MacromoleculeName: Bone marrow stromal antigen 2, Protein Nef chimera / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 29.964326 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: AP-1 complex subunit beta-1

MacromoleculeName: AP-1 complex subunit beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.458656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: ADP-ribosylation factor 1

MacromoleculeName: ADP-ribosylation factor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.9366 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EMRILMVGLD AAGKTTILYK LKLGEIVTTI PTIGFNVETV EYKNISFTVW DVGGLDKIRP LWRHYFQNTQ GLIFVVDSND RERVNEARE ELMRMLAEDE LRDAVLLVFA NKQDLPNAMN AAEITDKLGL HSLRHRNWYI QATCATSGDG LYEGLDWLSN Q LRNQK

UniProtKB: ADP-ribosylation factor 1

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Macromolecule #4: AP-1 complex subunit gamma-1

MacromoleculeName: AP-1 complex subunit gamma-1 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 66.401055 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #5: AP-1 complex subunit mu-1

MacromoleculeName: AP-1 complex subunit mu-1 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 48.475535 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #6: AP-1 complex subunit sigma-3

MacromoleculeName: AP-1 complex subunit sigma-3 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.99885 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIHFILLFSR QGKLRLQKWY ITLPDKERKK ITREIVQIIL SRGHRTSSFV DWKELKLVYK RYASLYFCCA IENQDNELLT LEIVHRYVE LLDKYFGNVC ELDIIFNFEK AYFILDEFII GGEIQETSKK IAVKAIEDSD MLQ

UniProtKB: AP-1 complex subunit sigma-3

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Macromolecule #7: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 6 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.07 mg/mL
BufferpH: 8
Details: 20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP
GridPretreatment - Type: PLASMA CLEANING / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 296 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 62.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: CRYOSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 11108
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 425 / Target criteria: Correlation coefficient
Output model

PDB-6cri:
Structure of the cargo bound AP-1:Arf1:tetherin-Nef stable closed trimer

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