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- EMDB-7453: Structure of the HIV-Nef dileucine mutant bound AP-1:Arf1 dimer m... -

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Database: EMDB / ID: 7453
TitleStructure of the HIV-Nef dileucine mutant bound AP-1:Arf1 dimer monomeric subunit
Map dataAP-1:Arf1:Tetherin-Nef dileucine mutant dimer monomeric subunit
SampleDimer of AP-1:Arf1:Tetherin-Nef dileucine mutant:
Function / homologyAdaptin C-terminal domain / HIV negative factor Nef / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / TBP domain superfamily / Synthesis of PIPs at the plasma membrane / Longin-like domain superfamily / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Gamma-adaptin ear (GAE) domain / Lysosome Vesicle Biogenesis / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain ...Adaptin C-terminal domain / HIV negative factor Nef / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / TBP domain superfamily / Synthesis of PIPs at the plasma membrane / Longin-like domain superfamily / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Gamma-adaptin ear (GAE) domain / Lysosome Vesicle Biogenesis / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Small GTPase superfamily, ARF/SAR type / Clathrin derived vesicle budding / Small GTP-binding protein domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Clathrin adaptor, mu subunit / Beta-adaptin appendage, C-terminal subdomain / Clathrin adaptor complex, small chain / Armadillo / MHC class II antigen presentation / Nef Mediated CD4 Down-regulation / Synthesis of PIPs at the Golgi membrane / Bone marrow stromal antigen 2 / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor complexes medium chain signature 2. / Gamma-adaptin ear (GAE) domain profile. / Mu homology domain (MHD) profile. / small GTPase Arf family profile. / Nef mediated downregulation of MHC class I complex cell surface expression / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Armadillo-like helical / Armadillo-type fold / Mu homology domain / Neutrophil degranulation / Adaptin N terminal region / Golgi Associated Vesicle Biogenesis / Clathrin adaptor complex small chain / Lysosome Vesicle Biogenesis / Adaptor complexes medium subunit family / Negative factor, (F-Protein) or Nef / MHC class II antigen presentation / Interferon alpha/beta signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / AP-1/2/4 complex subunit beta / ADP-ribosylation factor family / AP-2 complex subunit mu, C-terminal superfamily / Beta2-adaptin appendage, C-terminal sub-domain / HIV-1 Nef protein, core domain superfamily / Bone marrow stromal antigen 2 / HIV-1 Nef protein, anchor domain superfamily / Adaptor protein complex, sigma subunit / Adaptor protein complex AP-1, gamma subunit / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Neutrophil degranulation / P-loop containing nucleoside triphosphate hydrolase / Clathrin adaptor, mu subunit, conserved site / Golgi Associated Vesicle Biogenesis / Intra-Golgi traffic / AP complex, mu/sigma subunit / AP complex subunit beta / clathrin adaptor complex / negative regulation of plasmacytoid dendritic cell cytokine production / lysosomal membrane organization / Golgi to transport vesicle transport / synaptic vesicle budding / negative regulation of intracellular transport of viral material / positive regulation of late endosome to lysosome transport / mitotic cleavage furrow ingression / phospholipase D activator activity / regulation of phospholipid metabolic process / positive regulation of natural killer cell degranulation / negative regulation by symbiont of host T-cell mediated immune response / negative regulation of CD4 biosynthetic process / regulation of Arp2/3 complex-mediated actin nucleation / AP-1 adaptor complex / 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 / postsynaptic actin cytoskeleton organization / suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I / COPI-coated vesicle / response to interferon-alpha / dendritic spine organization / GTP-dependent protein binding / membrane coat / suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host adaptive immune response / positive regulation of calcium ion-dependent exocytosis / metalloendopeptidase inhibitor activity / suppression by virus of host autophagy / positive regulation of natural killer cell mediated cytotoxicity / long-term synaptic depression / determination of left/right symmetry / Golgi to plasma membrane transport / regulation of calcium-mediated signaling
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4.27 Å resolution
AuthorsBuffalo CZ / Morris KL / Hurley JH
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.
Validation ReportPDB-ID: 6d83

SummaryFull reportAbout validation report
DateDeposition: Feb 2, 2018 / Header (metadata) release: Mar 14, 2018 / Map release: Jul 25, 2018 / Last update: Aug 8, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0303
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0303
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6d83
  • Surface level: 0.0303
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7453.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.07 Å/pix.
= 273.152 Å
256 pix
1.07 Å/pix.
= 273.152 Å
256 pix
1.07 Å/pix.
= 273.152 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density
Contour Level:0.0303 (by author), 0.0303 (movie #1):
Minimum - Maximum-0.056176327 - 0.096912995
Average (Standard dev.)0.00032869034 (0.0033635767)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.0.0.
Limit255.255.255.
Spacing256256256
CellA=B=C: 273.152 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.152273.152273.152
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0630.1020.000

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Supplemental data

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Sample components

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Entire Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant

EntireName: Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant / Number of components: 1

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Component #1: protein, Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant

ProteinName: Dimer of AP-1:Arf1:Tetherin-Nef dileucine mutant / Recombinant expression: No
MassTheoretical: 230 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen 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
pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 294 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 39.7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500. X (nominal), 46849. X (calibrated) / Cs: 2.6 mm / Imaging mode: BRIGHT FIELD / Defocus: 750.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1989

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 85529
3D reconstructionResolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF

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