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- PDB-7ux3: Asymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide i... -

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Basic information

Entry
Database: PDB / ID: 7ux3
TitleAsymmetric unit of AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes
Components
  • (AP-1 complex subunit ...AP-1 transcription factor) x 4
  • ADP-ribosylation factor 1ARF1
  • HLA class I histocompatibility antigen, A alpha chain
  • Protein Nef
KeywordsVIRAL PROTEIN/PROTEIN TRANSPORT / nef / AP / HIV / trafficking / VIRAL PROTEIN / VIRAL PROTEIN-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


Glycosphingolipid transport / basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / AP-1 adaptor complex / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / Lysosome Vesicle Biogenesis / platelet dense granule organization ...Glycosphingolipid transport / basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / AP-1 adaptor complex / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / Lysosome Vesicle Biogenesis / platelet dense granule organization / regulation of receptor internalization / protein trimerization / melanosome assembly / symbiont-mediated suppression of host apoptosis / regulation of Arp2/3 complex-mediated actin nucleation / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / Intra-Golgi traffic / 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 / suppression by virus of host autophagy / clathrin adaptor activity / MHC class II antigen presentation / thioesterase binding / CD4 receptor binding / Nef Mediated CD4 Down-regulation / dendritic spine organization / determination of left/right symmetry / long-term synaptic depression / clathrin-coated vesicle / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / clathrin binding / Golgi medial cisterna / Golgi Associated Vesicle Biogenesis / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / host cell Golgi membrane / cell leading edge / antigen processing and presentation of exogenous peptide antigen via MHC class I / MHC class I protein binding / endoplasmic reticulum exit site / Synthesis of PIPs at the plasma membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / intracellular copper ion homeostasis / protection from natural killer cell mediated cytotoxicity / protein targeting / beta-2-microglobulin binding / COPI-mediated anterograde transport / detection of bacterium / T cell receptor binding / clathrin-coated pit / regulation of calcium-mediated signaling / 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 / sarcomere / small monomeric GTPase / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / trans-Golgi network membrane / kidney development / Nef mediated downregulation of MHC class I complex cell surface expression / virion component / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / cellular response to virus / MHC class I protein complex / SH3 domain binding / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of type II interferon production / Interferon alpha/beta signaling / E3 ubiquitin ligases ubiquitinate target proteins / heart development / T cell receptor signaling pathway / ER-Phagosome pathway
Similarity search - Function
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 ...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 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Rab subfamily of small GTPases / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Armadillo-like helical / Small GTP-binding protein domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Armadillo-type fold / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / HLA class I histocompatibility antigen, A alpha chain / AP-1 complex subunit gamma-1 / AP-1 complex subunit mu-1 / ADP-ribosylation factor 1 / AP-1 complex subunit beta-1 / Protein Nef / AP-1 complex subunit sigma-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.6 Å
AuthorsHooy, R.M. / Hurley, J.H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 AI152971 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI120691 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150476 United States
CitationJournal: Sci Adv / Year: 2022
Title: Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat.
Authors: Richard M Hooy / Yuichiro Iwamoto / Dan A Tudorica / Xuefeng Ren / James H Hurley /
Abstract: The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to ...The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to sequester major histocompatibility complex class I (MHC-I), evading immune detection. We found that AP-1:Arf1:Nef:MHC-I forms a coat on tubulated membranes without clathrin and determined its structure. The coat assembles via Arf1 dimer interfaces. AP-1-positive tubules are enriched in cells upon clathrin knockdown. Nef localizes preferentially to AP-1 tubules in cells, explaining how Nef sequesters MHC-I. Coat contact residues are conserved across Arf isoforms and the Arf-dependent AP complexes AP-1, AP-3, and AP-4. Thus, AP complexes can self-assemble with Arf1 into tubular coats without clathrin or other scaffolding factors. The AP-1:Arf1 coat defines the structural basis of a broader class of tubulovesicular membrane coats as an intermediate in clathrin vesicle formation from internal membranes and as an MHC-I sequestration mechanism in HIV-1 infection.
History
DepositionMay 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: ADP-ribosylation factor 1
H: ADP-ribosylation factor 1
N: Protein Nef
Y: HLA class I histocompatibility antigen, A alpha chain
B: AP-1 complex subunit beta-1
G: AP-1 complex subunit gamma-1
L: Protein Nef
M: AP-1 complex subunit mu-1
S: AP-1 complex subunit sigma-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,41713
Polymers334,3229
Non-polymers1,0954
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 4 molecules CHNL

#1: Protein ADP-ribosylation factor 1 / ARF1


Mass: 20800.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: glycine at position 2 is myristoylated - experimentally validated by mass spectrometry
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84077
#2: Protein Protein Nef / 3'ORF / Negative factor / F-protein


Mass: 24364.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: dileucine loop from adjacent protomer / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: nef / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q90VU7

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Protein/peptide , 1 types, 1 molecules Y

#3: Protein/peptide HLA class I histocompatibility antigen, A alpha chain / Human leukocyte antigen A / HLA-A


Mass: 4542.884 Da / Num. of mol.: 1 / Mutation: T345S, S349G, G355S, C363A
Source method: isolated from a genetically manipulated source
Details: C-terminal fragment / Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04439

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AP-1 complex subunit ... , 4 types, 4 molecules BGMS

#4: Protein AP-1 complex subunit beta-1 / AP-1 transcription factor / Adaptor protein complex AP-1 subunit beta-1 / Adaptor-related protein complex 1 subunit beta-1 / ...Adaptor protein complex AP-1 subunit beta-1 / Adaptor-related protein complex 1 subunit beta-1 / Beta-1-adaptin / Beta-adaptin 1 / Clathrin assembly protein complex 1 beta large chain / Golgi adaptor HA1/AP1 adaptin beta subunit


Mass: 104605.266 Da / Num. of mol.: 1 / Mutation: K359R,E476K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP1B1, ADTB1, BAM22, CLAPB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q10567
#5: Protein AP-1 complex subunit gamma-1 / AP-1 transcription factor / Adaptor protein complex AP-1 subunit gamma-1 / Adaptor-related protein complex 1 subunit gamma-1 / ...Adaptor protein complex AP-1 subunit gamma-1 / Adaptor-related protein complex 1 subunit gamma-1 / Clathrin assembly protein complex 1 gamma-1 large chain / Gamma-adaptin / Gamma1-adaptin / Golgi adaptor HA1/AP1 adaptin subunit gamma-1


Mass: 68062.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1g1, Adtg, Clapg1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22892
#6: Protein AP-1 complex subunit mu-1 / AP-1 transcription factor / AP-mu chain family member mu1A / Adaptor protein complex AP-1 subunit mu-1 / Adaptor-related ...AP-mu chain family member mu1A / Adaptor protein complex AP-1 subunit mu-1 / Adaptor-related protein complex 1 subunit mu-1 / Clathrin assembly protein complex 1 mu-1 medium chain 1 / Clathrin coat assembly protein AP47 / Clathrin coat-associated protein AP47 / Golgi adaptor HA1/AP1 adaptin mu-1 subunit / Mu-adaptin 1 / Mu1A-adaptin


Mass: 48475.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap1m1, Cltnm / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35585
#7: Protein AP-1 complex subunit sigma-3 / AP-1 transcription factor / Adaptor protein complex AP-1 subunit sigma-1C / Adaptor-related protein complex 1 subunit sigma-1C ...Adaptor protein complex AP-1 subunit sigma-1C / Adaptor-related protein complex 1 subunit sigma-1C / Clathrin assembly protein complex 1 sigma-1C small chain / Golgi adaptor HA1/AP1 adaptin sigma-1C subunit / Sigma 1C subunit of AP-1 clathrin / Sigma-adaptin 1C / Sigma1C-adaptin


Mass: 18305.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP1S3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96PC3

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Non-polymers , 2 types, 4 molecules

#8: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Complex of AP-1, Arf1, Nef and MHC-I cytosolic tail on a tubulated lipid bilayerCOMPLEXAsymmetric unit of the lattice on narrow membrane tubes#1-#70MULTIPLE SOURCES
2AP-1 heterotetramerCOMPLEXAll four subunits are co-expressed from the same plasmid. Assembly occurs in bacteria during expression.#4-#71MULTIPLE SOURCES
3Arf1, Nef and MHC-I cytosolic tailCOMPLEX#1-#31MULTIPLE SOURCES
Buffer solutionpH: 7.2
Details: HEPES/KOAc concentrated stocks are diluted to their final concentrations then pH'd to 7.2 with KOH prior to use in experiments.
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
2125 mMpotassium acetateKCH3COO1
32 mMmagnesium chloride1
41 mMDTT1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K
Details: 60 second wait, 3-5 second blot, 597 filter paper, 0.5 second drain. Sample was supplemented with 10nm BSA-gold fiducials. 3.5ul of the mixture was double-side blotted.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 42000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 3 e/Å2 / Avg electron dose per subtomogram: 123 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1
Details: Tilt images were collected in movie-mode. Each movie/tilt consisted of 3-4 frames each
EM imaging opticsEnergyfilter slit width: 25 eV
Image scansWidth: 5760 / Height: 4092

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20_4459refinement
PHENIX1.20_4459refinement
EM software
IDNameVersionCategory
1Dynamo1.1.532volume selection
2SerialEMimage acquisition
4NOVACTFCTF correction
7UCSF Chimera1.14model fitting
8UCSF ChimeraX1.3model fitting
13RELION3.1.13D reconstruction
14PHENIX1.20-4459model refinement
Image processingDetails: The images were gain-normalized
CTF correctionDetails: CTF was estimated on a per-tilt basis in IMOD (4.11) using CTFPLOTTER. The results were used as input to NOVACTF during 3DCTF correction.
Type: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16422 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionDetails: Tubes were annotated by tracing the center of the tube in Dynamo and recording the average apparent diameter. Initial subtomogram positions were picked using uniform radial and axial sampling.
Num. of tomograms: 31 / Num. of volumes extracted: 61864 / Reference model: Reference-free
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
16CM9

6cm9

6CM91
24EN2

4en2

B4EN22
34EN2

4en2

E4EN22
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 32.79 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00079004
ELECTRON MICROSCOPYf_angle_d0.240911257
ELECTRON MICROSCOPYf_chiral_restr0.08648
ELECTRON MICROSCOPYf_plane_restr0.00082227
ELECTRON MICROSCOPYf_dihedral_angle_d7.68322253

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