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- EMDB-7457: Structure of the HIV-Nef bound AP-1:Arf1 closed trimer monomeric ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7457
TitleStructure of the HIV-Nef bound AP-1:Arf1 closed trimer monomeric subunit
Map dataStructure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit
Sample
  • Complex: Closed trimer assembly of AP-1:Arf1:Tetherin-Nef
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 / : / AP-1 adaptor complex / endosome to melanosome transport / Lysosome Vesicle Biogenesis / mitotic cleavage furrow ingression / 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 / : / AP-1 adaptor complex / endosome to melanosome transport / Lysosome Vesicle Biogenesis / mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / protein trimerization / response to interferon-alpha / platelet dense granule organization / Glycosphingolipid transport / metalloendopeptidase inhibitor activity / regulation of receptor internalization / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / melanosome assembly / Intra-Golgi traffic / regulation of Arp2/3 complex-mediated actin nucleation / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / Golgi Associated Vesicle Biogenesis / symbiont-mediated suppression of host apoptosis / Synthesis of PIPs at the Golgi membrane / symbiont-mediated suppression of host autophagy / clathrin adaptor activity / positive regulation of leukocyte proliferation / MHC class II antigen presentation / CD4 receptor binding / thioesterase binding / Nef Mediated CD4 Down-regulation / dendritic spine organization / determination of left/right symmetry / long-term synaptic depression / clathrin-coated vesicle / azurophil granule membrane / COPI-dependent Golgi-to-ER retrograde traffic / clathrin binding / Lysosome Vesicle Biogenesis / negative regulation of viral genome replication / Golgi Associated Vesicle Biogenesis / cell leading edge / MHC class I protein binding / Synthesis of PIPs at the plasma membrane / B cell activation / host cell Golgi membrane / response to type II interferon / intracellular copper ion homeostasis / protein targeting / COPI-mediated anterograde transport / side of membrane / vesicle-mediated transport / clathrin-coated pit / regulation of calcium-mediated signaling / viral life cycle / Neutrophil degranulation / multivesicular body / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoplasmic vesicle membrane / negative regulation of cell migration / Nef mediated downregulation of MHC class I complex cell surface expression / sarcomere / small monomeric GTPase / trans-Golgi network membrane / kidney development / regulation of actin cytoskeleton organization / intracellular protein transport / trans-Golgi network / negative regulation of cell growth / response to virus / cellular response to virus / SH3 domain binding / virion component / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / synaptic vesicle / presynapse / heart development / ATPase binding / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / early endosome / neuron projection / postsynaptic density / symbiont-mediated suppression of host innate immune response / apical plasma membrane / protein domain specific binding / membrane raft / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / GTPase activity / intracellular membrane-bounded organelle / synapse / Neutrophil degranulation / protein kinase binding / GTP binding
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 / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / HIV negative factor Nef ...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 / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / HIV negative factor Nef / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / : / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / ADP-ribosylation factor 1-5 / 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 / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / Adaptor complexes medium subunit family / AP-2 complex subunit mu, C-terminal superfamily / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Small GTPase superfamily, ARF type / small GTPase Arf family profile. / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsMorris KL / Buffalo CZ / 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.
History
DepositionFeb 2, 2018-
Header (metadata) releaseMar 14, 2018-
Map releaseJul 25, 2018-
UpdateMay 15, 2019-
Current statusMay 15, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0726
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0726
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cm9
  • Surface level: 0.0726
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7457.png

Downloads & links

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Map

FileDownload / File: emd_7457.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 224 pix.
= 239.008 Å		1.07 Å/pix.
x 224 pix.
= 239.008 Å		1.07 Å/pix.
x 224 pix.
= 239.008 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0726 / Movie #1: 0.0726
Minimum - Maximum-0.23654956 - 0.30751687
Average (Standard dev.)0.0005696141 (±0.0090702735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 239.00801 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z239.008239.008239.008
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.2370.3080.001

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Supplemental data

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Sample components

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Entire : Closed trimer assembly of AP-1:Arf1:Tetherin-Nef

EntireName: Closed trimer assembly of AP-1:Arf1:Tetherin-Nef
Components
  • Complex: Closed trimer assembly of AP-1:Arf1:Tetherin-Nef

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Supramolecule #1: Closed trimer assembly of AP-1:Arf1:Tetherin-Nef

SupramoleculeName: Closed trimer assembly of AP-1:Arf1:Tetherin-Nef / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 230 KDa

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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

Concentration0.7 mg/mL
BufferpH: 8
Details: 20 mM Tris at pH 8.0, 200 mM NaCl, 5 mM MgCl2, and 0.5 mM TCEP
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV
DetailsAP-1:Arf1:Tetherin-Nef

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3712 pixel / Digitization - Dimensions - Height: 3840 pixel / Digitization - Frames/image: 3-38 / Number grids imaged: 1 / Number real images: 2200 / Average exposure time: 9.5 sec. / Average electron dose: 62.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 46849 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.6 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 252212
CTF correctionSoftware - Name: RELION
Startup modelType of model: OTHER / Details: Relion localized reconstruction (Ilca 2015)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 53841
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)

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Atomic model buiding 1

Initial model
PDB IDChain

4p6z


4hmy

chain_id: C

1o3y

chain_id: A, residue_range: 1001-1001

4en2

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6cm9:
Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit

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