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- PDB-8d9r: AP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide me... -

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Basic information

Entry
Database: PDB / ID: 8d9r
TitleAP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide 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 / 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 / protein trimerization / platelet dense granule organization ...basolateral protein secretion / 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 / protein trimerization / platelet dense granule organization / Glycosphingolipid transport / 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 / clathrin adaptor activity / : / 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 / COPI-dependent Golgi-to-ER retrograde traffic / positive regulation of memory T cell activation / Lysosome Vesicle Biogenesis / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / clathrin 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 / Golgi Associated Vesicle Biogenesis / CD8 receptor binding / cell leading edge / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / MHC class I protein binding / Synthesis of PIPs at the plasma membrane / endoplasmic reticulum exit site / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / intracellular copper ion homeostasis / protein targeting / 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 / COPI-mediated anterograde transport / T cell receptor binding / detection of bacterium / clathrin-coated pit / vesicle-mediated transport / regulation of calcium-mediated signaling / MHC class II antigen presentation / viral life cycle / Neutrophil degranulation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / trans-Golgi network membrane / small monomeric GTPase / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / trans-Golgi network / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / cytoplasmic vesicle membrane / MHC class I peptide loading complex / T cell mediated cytotoxicity / cellular response to virus / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / virion component / MHC class I protein complex / peptide antigen binding / SH3 domain binding / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / Interferon alpha/beta signaling / antibacterial humoral response / synaptic vesicle / presynapse / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling 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 / 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 ...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 / ADP-ribosylation factor 1-5 / Beta2-adaptin appendage, C-terminal sub-domain / 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 / 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/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / 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 / 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 / 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: 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

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


Theoretical massNumber of molelcules
Total (without water)2,143,05296
Polymers2,133,19860
Non-polymers9,85536
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "z"
d_2ens_1chain "1"
d_3ens_1chain "2"
d_4ens_1chain "Y"
d_5ens_1chain "y"
d_6ens_1chain "0"
d_1ens_2chain "3"
d_2ens_2chain "4"
d_3ens_2chain "5"
d_4ens_2chain "6"
d_5ens_2chain "7"
d_6ens_2chain "C"
d_7ens_2chain "H"
d_8ens_2chain "J"
d_9ens_2chain "K"
d_10ens_2chain "O"
d_11ens_2chain "P"
d_12ens_2chain "Q"
d_13ens_2chain "X"
d_14ens_2chain "Z"
d_15ens_2chain "a"
d_16ens_2chain "b"
d_17ens_2chain "c"
d_18ens_2chain "d"
d_1ens_3chain "A"
d_2ens_3chain "B"
d_3ens_3chain "D"
d_4ens_3chain "E"
d_5ens_3chain "F"
d_6ens_3chain "I"
d_1ens_4chain "V"
d_2ens_4chain "R"
d_3ens_4chain "T"
d_4ens_4chain "G"
d_5ens_4chain "U"
d_6ens_4chain "W"
d_1ens_5chain "e"
d_2ens_5chain "L"
d_3ens_5chain "f"
d_4ens_5chain "g"
d_5ens_5chain "h"
d_6ens_5chain "i"
d_1ens_6chain "M"
d_2ens_6chain "j"
d_3ens_6chain "k"
d_4ens_6chain "l"
d_5ens_6chain "m"
d_6ens_6chain "n"
d_1ens_7chain "r"
d_2ens_7chain "o"
d_3ens_7chain "p"
d_4ens_7chain "q"
d_5ens_7chain "N"
d_6ens_7chain "s"
d_1ens_8chain "t"
d_2ens_8chain "x"
d_3ens_8chain "u"
d_4ens_8chain "v"
d_5ens_8chain "w"
d_6ens_8chain "S"

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7
ens_8

NCS oper:
IDCodeMatrixVector
1given(-0.996721779259, -0.0144341936149, 0.0796074670255), (0.00514369750898, -0.993271394379, -0.115695632956), (0.0807417929419, -0.114906880402, 0.990089476618)657.699943348, 474.285593304, -0.0626326865575
2given(-0.997680541221, -0.0143187858104, 0.066547051345), (0.0071375279559, -0.994241762807, -0.106922274504), (0.0676948547859, -0.106199291257, 0.992037860755)439.789806054, 504.207646172, 10.0678640216
3given(0.99996932234, 0.00783102296378, -0.000171632695834), (-0.0078299337153, 0.999953522869, 0.00562532124053), (0.000215676738652, -0.00562380479621, 0.999984163026)-112.213219411, 17.5274860422, 5.30687340157
4given(0.999634792694, 0.0121186666595, -0.0241540711799), (-0.0121762553506, 0.999923360866, -0.00223857077189), (0.0241250915398, 0.00253185936793, 0.999705741529)-217.933022858, 37.8417813377, -1.81839073725
5given(-0.998639426475, -0.0123658396023, 0.0506594699992), (0.00670630414425, -0.993864642933, -0.110399714734), (0.0517138412264, -0.109909769991, 0.992595346093)553.905360916, 489.250323474, 13.0974389949
6given(0.999634821656, -0.0121806447437, 0.0241216754632), (0.0121230908213, 0.999923309947, 0.00253078930637), (-0.024150652216, -0.00223743585451, 0.99970582667)218.359513446, -35.1937449074, -3.36220574639
7given(-0.99964816584, -0.000321109179538, 0.0265224701198), (-0.00267148096326, -0.993623244418, -0.112719613832), (0.0263895381132, -0.112750809496, 0.993272795981)336.109312291, 526.062286515, 24.9202842925
8given(-0.998456022458, -0.00247617696761, 0.0554927000976), (-0.00409896555248, -0.992997987579, -0.118060133602), (0.0553964773059, -0.118105314073, 0.991454671223)440.300324915, 510.755337047, 18.2865875155
9given(-0.999097063564, -0.00231718947733, 0.0424227322315), (-0.00233285193414, -0.994013176032, -0.109235359092), (0.042421873826, -0.109235692459, 0.993110239658)222.217980112, 541.116300293, 25.2521196585
10given(-0.898188731961, 0.248889479306, -0.362368636707), (-0.059889406023, -0.88588752195, -0.46001799693), (-0.435511493332, -0.391480938928, 0.810600033081)396.974715772, 441.327596157, 190.824769321
11given(0.958773027461, -0.112848352776, 0.260805542673), (0.0694779382266, 0.983005037791, 0.169923252612), (-0.275548721487, -0.144797599959, 0.950319186975)45.4683125301, -37.6866997204, 94.6183214718
12given(-0.887721428354, 0.254529969061, -0.383621115804), (-0.0525646090163, -0.883856545612, -0.464795190011), (-0.457370339572, -0.392443756006, 0.797997663438)288.410182351, 457.953608479, 199.219673221
13given(-0.897788734915, 0.255736636984, -0.358572391526), (-0.0644789983333, -0.881696174626, -0.467390965279), (-0.435680899552, -0.396497954793, 0.808066535386)505.892052597, 426.725248444, 187.809309389
14given(0.875295397551, -0.264564915611, 0.40480041064), (0.106155338374, 0.921776651109, 0.372905952763), (-0.471793398811, -0.283431139607, 0.834911838423)52.9373558153, 47.8024410996, 178.776099869
15given(0.861099794905, -0.273726550379, 0.428463439317), (0.109832632647, 0.92295637625, 0.368901504938), (-0.496431199684, -0.270601742709, 0.824821653949)162.256635938, 31.3063014652, 177.694239854
16given(0.867639360378, -0.26889800945, 0.418205452902), (0.104280237243, 0.920841107303, 0.375735661365), (-0.486135343751, -0.282392485053, 0.82699873757)-58.5423215263, 63.4703437005, 185.308660492
17given(0.965388978816, -0.105256659952, 0.238631840112), (0.0674750818422, 0.98459333224, 0.161316717793), (-0.251934977544, -0.139631678514, 0.957617753305)-62.6730555139, -18.7588092016, 90.8090195238
18given(0.999703491312, -0.00434160602392, 0.0239599648674), (0.00415197088632, 0.999959708928, 0.00795874727393), (-0.0239935532398, -0.00785690635965, 0.999681238408)105.865070615, -19.390514715, 2.1868861284
19given(0.958137746779, -0.120579570725, 0.259677926134), (0.0785362818633, 0.982888414044, 0.166620580867), (-0.275325463095, -0.139251329118, 0.951212361521)158.128581628, -54.4811385569, 88.9753598369
20given(-0.971752810433, 0.101198595826, -0.213202531923), (-0.0412237493048, -0.962294198385, -0.268868886722), (-0.232372713349, -0.252485088583, 0.939283877289)401.175384652, 534.632747735, 115.580203173
21given(-0.978045907358, 0.0949086170742, -0.185522390844), (-0.0412168268799, -0.960782346473, -0.274223368604), (-0.204272798682, -0.260556399099, 0.943601073869)507.962191453, 518.919176426, 107.063762867
22given(-0.975360986813, 0.0969581394281, -0.198166759579), (-0.0418040642005, -0.963200254362, -0.265514011331), (-0.216618017763, -0.250687832164, 0.943521194879)288.730236148, 549.989777169, 114.82641419
23given(0.999703481175, -0.00434476530224, 0.0239598151153), (0.0041551194823, 0.999959691648, 0.00795927513784), (-0.0239934305171, -0.00785735916835, 0.999681237795)105.86579674, -19.3911503158, 2.18698957679
24given(0.999634856698, -0.0121810775715, 0.0241200046218), (0.0121235513017, 0.999923306855, 0.00252980458166), (-0.0241489705286, -0.00223646072703, 0.999705869477)218.360004231, -35.1935697064, -3.36271380255
25given(-0.999648157245, -0.000321724524283, 0.026522786612), (-0.00267088469038, -0.993623332897, -0.112718848015), (0.0263899240489, -0.11275002801, 0.993272874437)336.109378915, 526.061977435, 24.9200782842
26given(-0.998455973959, -0.00247500546956, 0.0554936249765), (-0.00410031017789, -0.992997833165, -0.118061385669), (0.0553972519314, -0.118106636891, 0.991454470362)440.299825593, 510.755817459, 18.286805386
27given(-0.999097040236, -0.00231644304433, 0.042423322404), (-0.002333648274, -0.994013202153, -0.109235104395), (0.0424223794465, -0.109235470604, 0.993110242463)222.217689135, 541.116377412, 25.2520291348
28given(-0.998456035811, -0.00410020977972, 0.0553961445549), (-0.0024749526258, -0.992997879088, -0.118106251892), (0.0554925144618, -0.118061002902, 0.991454578099)440.701510006, 510.428852224, 17.7364200855
29given(-0.996722777947, 0.0051491527119, 0.0807291158661), (-0.0144390517531, -0.993270031367, -0.114918051549), (0.0795940808518, -0.115707091458, 0.990089213798)653.110727541, 480.583973958, 2.58441435616
30given(-0.996819601729, -0.00261362506808, 0.0796482929675), (-0.00618168491038, -0.993914541723, -0.109980318796), (0.079451043922, -0.110122898232, 0.990737341027)544.643879695, 492.989452369, 5.33313475377
31given(0.999577339508, 0.00128631347763, -0.029042860406), (-0.00112850823154, 0.999984515859, 0.00544926712687), (0.029049420168, -0.00541418882991, 0.999563313526)-104.13060595, 15.7115181965, -3.38380797495
32given(0.999914372394, 0.0013885339189, -0.0130122962097), (-0.00127188609048, 0.99995897401, 0.00896842256908), (0.0130242153262, -0.00895110446597, 0.999875115974)-218.515768118, 30.7775394023, 5.80474062152
33given(0.999703381592, -0.00432841022137, 0.0239669292762), (0.00413853101926, 0.999959702973, 0.00796649175746), (-0.0240004457246, -0.00786494086911, 0.999681009778)105.860669612, -19.3910261264, 2.18925916651
34given(0.999635679646, -0.0121681205082, 0.0240924225062), (0.0121116221894, 0.999923552316, 0.00248960454806), (-0.0241208745045, -0.00219689921543, 0.999706635492)218.363705064, -35.1829569532, -3.37392458644
35given(-0.999647251056, -0.000331124741207, 0.0265568034957), (-0.00266449920922, -0.993627102028, -0.112685769107), (0.0264248727427, -0.112716779903, 0.993275718836)336.103333034, 526.054398806, 24.9089548651
36given(-0.99845615374, -0.00246811633616, 0.055490697066), (-0.00410721192254, -0.992996959474, -0.118068494047), (0.0553935002446, -0.118114126497, 0.991453787754)440.299158676, 510.758047111, 18.2889500721
37given(-0.999096331079, -0.00232076260799, 0.04243978422), (-0.00233052312475, -0.994014827, -0.109220384385), (0.0424392493535, -0.109220592217, 0.993111158104)222.214728622, 541.11297264, 25.2470560318
38given(0.999703489687, 0.00415478411078, -0.0239931339652), (-0.00434444088918, 0.999959688662, -0.0078579185216), (0.0239595188149, 0.00795982531997, 0.999681240516)-105.701369735, 19.8675968838, -4.56848558159
39given(0.999969282397, -0.00783481582576, 0.0002234346861), (0.00783594785087, 0.999953508967, -0.0056194151293), (-0.000179397215805, 0.00562099333689, 0.999984186)112.345002939, -16.620356969, -5.42182875359
40given(-0.998714921879, -0.00426398443225, 0.0505007252808), (-0.00105390621164, -0.99449156529, -0.104811334546), (0.0506694592316, -0.104729866821, 0.993209072098)441.646222321, 507.118403987, 15.353049108
41given(-0.996819604757, -0.00618131216412, 0.0794510349282), (-0.00261392327418, -0.993914640801, -0.110121996928), (0.0796482452811, -0.109979444362, 0.99073744193)545.535383883, 492.000066322, 5.55529037689
42given(-0.997774298169, -0.00613018670423, 0.0663993277426), (-0.000631197033143, -0.994852393924, -0.101332699041), (0.066678718524, -0.101149073726, 0.992634279773)327.583909536, 522.113154776, 14.0605144386
43given(-0.998456032652, -0.00409990757865, 0.0553962238693), (-0.00247520261677, -0.992998005862, -0.118105180779), (0.0554925601603, -0.118059947115, 0.991454701262)440.701378498, 510.428748739, 17.7360206835
44given(-0.996722865848, 0.00514785803806, 0.0807281131562), (-0.0144376116367, -0.993270100012, -0.114917639166), (0.079593241336, -0.115706559792, 0.99008934342)653.111357215, 480.583524154, 2.5844366066
45given(0.999577329247, 0.00128873867323, -0.0290431060441), (-0.00113098356666, 0.999984522526, 0.00544753008129), (0.0290496769729, -0.00541238029399, 0.999563315857)-104.131263912, 15.712648998, -3.38448109908
46given(-0.996819753023, -0.00261491358922, 0.0796463571645), (-0.00618016685528, -0.993914577032, -0.109980085018), (0.0794492638122, -0.110122548962, 0.990737522601)544.64475247, 492.989037768, 5.33343492159
47given(0.999914354574, 0.00138913484231, -0.0130136013752), (-0.00127249955845, 0.99995898989, 0.00896656472624), (0.0130255234535, -0.00894923697898, 0.99987511565)-218.515621309, 30.7780908797, 5.8038276896
48given(-0.999096983401, -0.00231687177058, 0.0424246374782), (-0.0023333937899, -0.99401313034, -0.109235763304), (0.0424237319596, -0.109236114983, 0.993110113809)222.21746132, 541.116496331, 25.2520367115
49given(0.99963490938, -0.0121801463532, 0.0241182914699), (0.0121226259945, 0.99992331832, 0.00252970745197), (-0.0241472542458, -0.00223640685239, 0.999705911054)218.36023852, -35.1934273117, -3.36290159745
50given(-0.99964817234, -0.000325593566878, 0.0265221704527), (-0.00266699669918, -0.993623226971, -0.112719873809), (0.0263897454573, -0.112750950381, 0.99327277448)336.110348941, 526.061775608, 24.9203085192
51given(-0.998455828255, -0.0024758745998, 0.0554962076979), (-0.00409968008768, -0.992997988315, -0.118060102595), (0.0553999246124, -0.118105314218, 0.991454478585)440.299365267, 510.755483695, 18.2862519237
52given(0.999703509306, -0.00434316921508, 0.0239589307343), (0.00415355234821, 0.99995970559, 0.00795834142844), (-0.0239925297468, -0.00785646718126, 0.999681266424)105.8656895, -19.3907715101, 2.18671159125

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Components

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Protein , 2 types, 30 molecules CHZJX3Ka4Ob5Pc6Qd7NLoepfqgrhsi

#1: Protein
ADP-ribosylation factor 1


Mass: 20800.902 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Details: N-terminal myristoylation at Gly-2 / 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.: 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 Yyz012

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


Mass: 4558.884 Da / Num. of mol.: 6 / Fragment: MHC-I cytosolic tail (HLA-A/B) / 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 BADEFIGRTUVWMjklmnStuvwx

#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, 36 molecules

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


Mass: 523.180 Da / Num. of mol.: 18 / 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.: 18 / 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 form a lattice on MHC-I lipopeptide incorporated wide membrane tubes
Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
31Human immunodeficiency virus 111676
41Mus musculus (house mouse)10090
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: ETHANE

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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: 121 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: 2454 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 13 / Num. of volumes extracted: 4208
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 35.06 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.000758542
ELECTRON MICROSCOPYf_angle_d0.296173248
ELECTRON MICROSCOPYf_chiral_restr0.091672
ELECTRON MICROSCOPYf_plane_restr0.000814442
ELECTRON MICROSCOPYf_dihedral_angle_d3.067314676

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