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- PDB-8d9t: AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow ... -

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Basic information

Entry
Database: PDB / ID: 8d9t
TitleAP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes, centered on gamma-Arf1
Components
  • (AP-1 complex subunit ...) x 4
  • ADP ribosylation factor 1
  • HLA class I histocompatibility antigen, A alpha chain
  • Protein Nef
KeywordsVIRAL PROTEIN/PROTEIN TRANSPORT / nef / AP / trafficking / VIRAL PROTEIN-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


basolateral protein secretion / endosome to melanosome transport / Lysosome Vesicle Biogenesis / AP-1 adaptor complex / mitotic cleavage furrow ingression / protein trimerization / platelet dense granule organization / negative regulation of glycoprotein biosynthetic process / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / melanosome assembly ...basolateral protein secretion / endosome to melanosome transport / Lysosome Vesicle Biogenesis / AP-1 adaptor complex / mitotic cleavage furrow ingression / protein trimerization / platelet dense granule organization / negative regulation of glycoprotein biosynthetic process / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / melanosome assembly / 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 autophagy / clathrin adaptor activity / symbiont-mediated suppression of host apoptosis / MHC class II antigen presentation / thioesterase binding / CD4 receptor binding / determination of left/right symmetry / clathrin-coated vesicle / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / clathrin binding / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / cell leading edge / endoplasmic reticulum exit site / MHC class I protein binding / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / host cell Golgi membrane / protection from natural killer cell mediated cytotoxicity / 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 / intracellular copper ion homeostasis / detection of bacterium / protein targeting / T cell receptor binding / vesicle-mediated transport / viral life cycle / clathrin-coated pit / regulation of calcium-mediated signaling / Neutrophil degranulation / MHC class II antigen presentation / cytoplasmic vesicle membrane / Nef mediated downregulation of MHC class I complex cell surface expression / sarcomere / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / kidney development / trans-Golgi network / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / cellular response to virus / peptide antigen binding / SH3 domain binding / positive regulation of T cell mediated cytotoxicity / virion component / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / synaptic vesicle / antibacterial humoral response / protein transport / T cell receptor signaling pathway / presynapse / E3 ubiquitin ligases ubiquitinate target proteins / heart development / ER-Phagosome pathway / ATPase binding / early endosome membrane / early endosome / defense response to Gram-positive bacterium / immune response / symbiont-mediated suppression of host innate immune response / signaling receptor binding / Golgi membrane / protein domain specific binding / lysosomal membrane / innate immune response / external side of plasma membrane
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 / 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 / HIV-1 Nef protein, core domain superfamily ...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 / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / Adaptor protein complex, sigma subunit / : / 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 / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Small GTPase superfamily, ARF type / Small GTPase Arf domain 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 / 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 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Rab subfamily of small GTPases / 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 / ADP-ribosylation factor / HLA class I histocompatibility antigen, A alpha chain / AP-1 complex subunit gamma-1 / AP-1 complex subunit mu-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: 20 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
DepositionJun 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.2Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
J: ADP ribosylation factor 1
X: ADP ribosylation factor 1
n: Protein Nef
x: HLA class I histocompatibility antigen, A alpha chain
A: AP-1 complex subunit beta-1
R: AP-1 complex subunit gamma-1
d: Protein Nef
i: AP-1 complex subunit mu-1
s: AP-1 complex subunit sigma-3
K: ADP ribosylation factor 1
Z: ADP ribosylation factor 1
o: Protein Nef
y: HLA class I histocompatibility antigen, A alpha chain
D: AP-1 complex subunit beta-1
T: AP-1 complex subunit gamma-1
e: Protein Nef
j: AP-1 complex subunit mu-1
t: AP-1 complex subunit sigma-3
O: ADP ribosylation factor 1
a: ADP ribosylation factor 1
p: Protein Nef
z: HLA class I histocompatibility antigen, A alpha chain
E: AP-1 complex subunit beta-1
U: AP-1 complex subunit gamma-1
f: Protein Nef
k: AP-1 complex subunit mu-1
u: AP-1 complex subunit sigma-3
P: ADP ribosylation factor 1
b: ADP ribosylation factor 1
q: Protein Nef
0: HLA class I histocompatibility antigen, A alpha chain
F: AP-1 complex subunit beta-1
V: AP-1 complex subunit gamma-1
g: Protein Nef
l: AP-1 complex subunit mu-1
v: AP-1 complex subunit sigma-3
Q: ADP ribosylation factor 1
c: ADP ribosylation factor 1
r: Protein Nef
1: HLA class I histocompatibility antigen, A alpha chain
I: AP-1 complex subunit beta-1
W: AP-1 complex subunit gamma-1
h: Protein Nef
m: AP-1 complex subunit mu-1
w: AP-1 complex subunit sigma-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,014,86678
Polymers2,008,29654
Non-polymers6,57024
Water00
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, 24 molecules CHJXKZOaPbQcNLndoepfqgrh

#1: Protein
ADP ribosylation factor 1


Mass: 20800.902 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: N-terminal myristoylation on Gly-2 / Source: (gene. exp.) Homo sapiens (human) / Gene: ARF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8C2UGL4
#2: Protein
Protein Nef / 3'ORF / Negative factor / F-protein


Mass: 24364.404 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: N-terminal myristoylation at Gly-2 / 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, 6 molecules Yxyz01

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


Mass: 4542.884 Da / Num. of mol.: 6 / Mutation: T345S, S349G, G355S, C363A
Source method: isolated from a genetically manipulated source
Details: conjugated to MPB-PE lipid / 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, 24 molecules BADEFIGRTUVWMijklmSstuvw

#4: Protein
AP-1 complex subunit beta-1 / 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: 104736.461 Da / Num. of mol.: 6 / 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 / 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: 68194.094 Da / Num. of mol.: 6
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-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: 48606.730 Da / Num. of mol.: 6
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 / 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.: 6
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, 24 molecules

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


Mass: 523.180 Da / Num. of mol.: 12 / 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.: 12 / 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

ComponentName: AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated narrow membrane tubes
Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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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 FIELD / Nominal defocus max: 4500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 3 e/Å2 / Avg electron dose per subtomogram: 123 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20_4459refinement
PHENIX1.20_4459refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 20 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8144 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 38 / Num. of volumes extracted: 23154
Atomic model buildingProtocol: RIGID BODY FIT
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_d0.000554024
ELECTRON MICROSCOPYf_angle_d0.215767542
ELECTRON MICROSCOPYf_chiral_restr0.077348
ELECTRON MICROSCOPYf_plane_restr0.000813362
ELECTRON MICROSCOPYf_dihedral_angle_d5.176913518

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