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

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基本情報

登録情報
データベース: PDB / ID: 8d9r
タイトルAP-1, Arf1, Nef lattice on MHC-I lipopeptide incorporated wide membrane tubes, centered on gamma-Arf1
要素
  • (AP-1 complex subunit ...) x 4
  • ADP-ribosylation factor 1
  • HLA class I histocompatibility antigen, A alpha chain
  • Protein Nef
キーワードVIRAL PROTEIN/PROTEIN TRANSPORT / nef / AP / trafficking / VIRAL PROTEIN-PROTEIN TRANSPORT complex
機能・相同性
機能・相同性情報


basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization ...basolateral protein secretion / perturbation by virus of host immune response / negative regulation of CD4 production / mitotic cleavage furrow ingression / endosome to melanosome transport / trans-Golgi Network Vesicle Budding / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / protein trimerization / regulation of receptor internalization / Glycosphingolipid transport / melanosome assembly / 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 apoptosis / 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 / clathrin adaptor activity / suppression by virus of host autophagy / MHC class II antigen presentation / CD4 receptor binding / Nef Mediated CD4 Down-regulation / thioesterase binding / 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 / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / clathrin binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / Golgi Associated Vesicle Biogenesis / CD8 receptor binding / cell leading edge / host cell Golgi membrane / MHC class I protein binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / 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 / protection from natural killer cell mediated cytotoxicity / intracellular copper ion homeostasis / protein targeting / beta-2-microglobulin binding / COPI-mediated anterograde transport / T cell receptor binding / detection of bacterium / clathrin-coated pit / vesicle-mediated transport / regulation of calcium-mediated signaling / 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 / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / kidney development / virion component / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / cytoplasmic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / trans-Golgi network / 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 / Interferon alpha/beta signaling / positive regulation of type II interferon production / E3 ubiquitin ligases ubiquitinate target proteins / heart development / T cell receptor signaling pathway / ER-Phagosome pathway
類似検索 - 分子機能
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
類似検索 - ドメイン・相同性
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
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
Mus musculus (ハツカネズミ)
手法電子顕微鏡法 / サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 20 Å
データ登録者Hooy, R.M. / Hurley, J.H.
資金援助 米国, 3件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32 AI152971 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI120691 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150476 米国
引用ジャーナル: Sci Adv / 年: 2022
タイトル: Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat.
著者: Richard M Hooy / Yuichiro Iwamoto / Dan A Tudorica / Xuefeng Ren / James H Hurley /
要旨: 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.
履歴
登録2022年6月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年11月9日Provider: repository / タイプ: Initial release
改定 1.12022年12月21日Group: Database references / カテゴリ: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
改定 1.22024年6月12日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
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
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,143,05296
ポリマ－2,133,19860
非ポリマー9,85536
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法
タイプ名称対称操作数
identity operation1_5551
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
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アンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7
ens_8

NCS oper:
IDCodeMatrixベクター
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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要素

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タンパク質 , 2種, 30分子 CHZJX3Ka4Ob5Pc6Qd7NLoepfqgrhsi

#1: タンパク質
ADP-ribosylation factor 1


分子量: 20800.902 Da / 分子数: 18 / 由来タイプ: 組換発現 / 詳細: N-terminal myristoylation at Gly-2 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ARF1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P84077
#2: タンパク質
Protein Nef / 3'ORF / Negative factor / F-protein


分子量: 24364.404 Da / 分子数: 12 / 由来タイプ: 組換発現 / 詳細: N-terminal myristoylation at Gly-2
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
遺伝子: nef / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q90VU7

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タンパク質・ペプチド , 1種, 6分子 Yyz012

#3: タンパク質・ペプチド
HLA class I histocompatibility antigen, A alpha chain / Human leukocyte antigen A / HLA-A


分子量: 4558.884 Da / 分子数: 6 / Fragment: MHC-I cytosolic tail (HLA-A/B) / Mutation: T345S, S349G, G355S, C363A / 由来タイプ: 組換発現 / 詳細: conjugated to MPB-PE lipid / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-A, HLAA / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P04439

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AP-1 complex subunit ... , 4種, 24分子 BADEFIGRTUVWMjklmnStuvwx

#4: タンパク質
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


分子量: 104736.461 Da / 分子数: 6 / Mutation: K359R,E476K / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: AP1B1, ADTB1, BAM22, CLAPB2 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q10567
#5: タンパク質
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


分子量: 68194.094 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Ap1g1, Adtg, Clapg1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P22892
#6: タンパク質
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


分子量: 48606.730 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Ap1m1, Cltnm / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P35585
#7: タンパク質
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


分子量: 18305.273 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: AP1S3 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q96PC3

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非ポリマー , 2種, 36分子

#8: 化合物
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP


分子量: 523.180 Da / 分子数: 18 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: GTP, エネルギー貯蔵分子*YM
#9: 化合物
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 18 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: サブトモグラム平均法

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試料調製

構成要素名称: AP-1, Arf1, Nef form a lattice on MHC-I lipopeptide incorporated wide membrane tubes
タイプ: COMPLEX / Entity ID: #1-#7 / 由来: MULTIPLE SOURCES
分子量実験値: NO
由来(天然)
IDEntity assembly-ID生物種Ncbi tax-ID
21Homo sapiens (ヒト)9606
31Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)11676
41Mus musculus (ハツカネズミ)10090
由来(組換発現)生物種: Escherichia coli BL21(DE3) (大腸菌)
緩衝液pH: 7.2
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: ETHANE

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / 最大 デフォーカス（公称値）: 4500 nm / 最小 デフォーカス（公称値）: 1500 nm
撮影電子線照射量: 3 e/Å2 / Avg electron dose per subtomogram: 121 e/Å2
フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)

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解析

ソフトウェア
名称バージョン分類NB
phenix.real_space_refine1.20_4459精密化
PHENIX1.20_4459精密化
CTF補正タイプ: PHASE FLIPPING ONLY
対称性点対称性: C1 (非対称)
3次元再構成解像度: 20 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 2454 / 対称性のタイプ: POINT
EM volume selectionNum. of tomograms: 13 / Num. of volumes extracted: 4208
精密化交差検証法: NONE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
原子変位パラメータBiso mean: 35.06 Å2
拘束条件
Refine-IDタイプDev ideal数
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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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る