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- PDB-8tku: ZIG-4-INS-6 complex, primitive monoclinic form -

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基本情報

登録情報
データベース: PDB / ID: 8tku
タイトルZIG-4-INS-6 complex, primitive monoclinic form
要素
  • Probable insulin-like peptide beta-type 5
  • Zwei Ig domain protein zig-4
キーワードSIGNALING PROTEIN/PROTEIN BINDING / NEUROPEPTIDE / SIGNALING PROTEIN / PROTEIN BINDING / SIGNALING PROTEIN-PROTEIN BINDING complex
機能・相同性
機能・相同性情報


negative regulation of dauer entry / dauer larval development / cellular response to salt / regulation of synaptic assembly at neuromuscular junction / chemosensory behavior / olfactory learning / neuron development / insulin receptor binding / hormone activity / insulin receptor signaling pathway ...negative regulation of dauer entry / dauer larval development / cellular response to salt / regulation of synaptic assembly at neuromuscular junction / chemosensory behavior / olfactory learning / neuron development / insulin receptor binding / hormone activity / insulin receptor signaling pathway / extracellular space / extracellular region
類似検索 - 分子機能
Nematode insulin-like peptide, beta type / : / Nematode insulin-related peptide beta type / : / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain ...Nematode insulin-like peptide, beta type / : / Nematode insulin-related peptide beta type / : / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
Zwei Ig domain protein zig-4 / Probable insulin-like peptide beta-type 5
類似検索 - 構成要素
生物種Caenorhabditis elegans (センチュウ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.35 Å
データ登録者Cheng, S. / Baltrusaitis, E. / Aziz, Z. / Nawrocka, W.I. / Ozkan, E.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097161 米国
引用ジャーナル: Biorxiv / 年: 2024
タイトル: Nematode Extracellular Protein Interactome Expands Connections between Signaling Pathways.
著者: Nawrocka, W.I. / Cheng, S. / Hao, B. / Rosen, M.C. / Cortes, E. / Baltrusaitis, E.E. / Aziz, Z. / Kovacs, I.A. / Ozkan, E.
履歴
登録2023年7月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年8月28日Provider: repository / タイプ: Initial release
改定 1.12024年10月16日Group: Database references / Structure summary
カテゴリ: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Zwei Ig domain protein zig-4
B: Probable insulin-like peptide beta-type 5
C: Zwei Ig domain protein zig-4
D: Probable insulin-like peptide beta-type 5
E: Zwei Ig domain protein zig-4
F: Probable insulin-like peptide beta-type 5
G: Zwei Ig domain protein zig-4
H: Probable insulin-like peptide beta-type 5


分子量 (理論値)分子数
合計 (水以外)120,7488
ポリマ－120,7488
非ポリマー00
水70339
1
A: Zwei Ig domain protein zig-4
B: Probable insulin-like peptide beta-type 5


分子量 (理論値)分子数
合計 (水以外)30,1872
ポリマ－30,1872
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Zwei Ig domain protein zig-4
D: Probable insulin-like peptide beta-type 5


分子量 (理論値)分子数
合計 (水以外)30,1872
ポリマ－30,1872
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Zwei Ig domain protein zig-4
F: Probable insulin-like peptide beta-type 5


分子量 (理論値)分子数
合計 (水以外)30,1872
ポリマ－30,1872
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Zwei Ig domain protein zig-4
H: Probable insulin-like peptide beta-type 5


分子量 (理論値)分子数
合計 (水以外)30,1872
ポリマ－30,1872
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)73.839, 55.739, 149.945
Angle α, β, γ (deg.)90.000, 93.780, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 43 through 150 or resid 154...
d_2ens_1(chain "C" and (resid 43 through 233 or (resid 234...
d_3ens_1(chain "E" and (resid 43 through 233 or (resid 234...
d_4ens_1chain "G"
d_1ens_2(chain "B" and resid 62 through 112)
d_2ens_2(chain "D" and resid 62 through 112)
d_3ens_2(chain "F" and resid 62 through 112)
d_4ens_2(chain "H" and resid 62 through 112)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PROPROGLUGLUAA43 - 1503 - 110
d_12ens_1CYSCYSHISHISAA154 - 249114 - 209
d_21ens_1PROPROHISHISCC43 - 2493 - 209
d_31ens_1PROPROHISHISEE43 - 2493 - 209
d_41ens_1PROPROHISHISGG43 - 2493 - 209
d_11ens_2PROPROPROPROBB62 - 1124 - 54
d_21ens_2PROPROPROPRODD62 - 1124 - 54
d_31ens_2PROPROPROPROFF62 - 1124 - 54
d_41ens_2PROPROPROPROHH62 - 1124 - 54

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.993335918358, 0.0963661180079, -0.0632243987727), (-0.109918109867, -0.957075754114, 0.268186520934), (-0.0346664452093, 0.273348810474, 0.961290104697)45.4907129287, 34.2077528125, 0.00899187516622
2given(0.990295577877, -0.115258876393, 0.0776534600057), (-0.138461332408, -0.866338511784, 0.479881279513), (0.0119636058976, -0.485976310546, -0.873890094761)-5.58547031341, 25.1084079414, 78.3653393089
3given(-0.999965426385, -0.00805582797323, 0.00206147263171), (-0.00711671516513, 0.957327452616, 0.288917809823), (-0.0043009765175, 0.288893149977, -0.957351685379)39.9487228549, -9.53800733938, 69.4017890868
4given(-0.997610670265, 0.0679381988571, -0.0125439910096), (-0.0688113479686, -0.960930694019, 0.268099234768), (0.00616027313849, 0.268321826224, 0.96330963278)44.340168732, 33.780652904, -1.15081259072
5given(0.994042002441, -0.100369576781, 0.0425022992412), (-0.108588122518, -0.878143250381, 0.465910990918), (-0.0094401817716, -0.467750339248, -0.883810218939)-4.60906964325, 25.1092508237, 79.1279371536
6given(-0.99932941638, -0.0111872591378, 0.034864922055), (-0.00108768429732, 0.960831788273, 0.277130098668), (-0.0365996516348, 0.276906337735, -0.96019963842)39.1706154356, -9.41396576138, 69.932825615

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要素

#1: タンパク質
Zwei Ig domain protein zig-4


分子量: 23689.566 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Caenorhabditis elegans (センチュウ)
遺伝子: zig-4 / 細胞株 (発現宿主): High Five cells / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: G5ECB1
#2: タンパク質
Probable insulin-like peptide beta-type 5 / INS-6


分子量: 6497.392 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Caenorhabditis elegans (センチュウ)
遺伝子: ins-6 / 細胞株 (発現宿主): High Five cells / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P56174
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 39 / 由来タイプ: 天然 / 式: H2O
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.55 Å3/Da / 溶媒含有率: 51.76 %
結晶化温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.2 M sodium iodide, 0.1 M bis-tris propane, pH 6.5, 20% PEG 3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-E / 波長: 0.97918 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年10月25日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97918 Å / 相対比: 1
反射解像度: 2.35→200 Å / Num. obs: 50159 / % possible obs: 97.9 % / 冗長度: 3.1 % / Biso Wilson estimate: 66.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 10.7
反射 シェル解像度: 2.35→2.49 Å / 冗長度: 3.1 % / Rmerge(I) obs: 1.248 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 7983 / CC1/2: 0.463 / Rsym value: 1.248 / % possible all: 97.1

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDS20190806データ削減
XDS20190806データスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.35→74.81 Å / SU ML: 0.4344 / 交差検証法: FREE R-VALUE / 位相誤差: 31.456
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2398 1977 3.95 %
Rwork0.1966 48119 -
obs0.1983 50096 97.79 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 83.08 Å2
精密化ステップサイクル: LAST / 解像度: 2.35→74.81 Å
タンパク質核酸リガンド溶媒全体
原子数7755 0 0 39 7794
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0087895
X-RAY DIFFRACTIONf_angle_d1.001610742
X-RAY DIFFRACTIONf_chiral_restr0.05731247
X-RAY DIFFRACTIONf_plane_restr0.00811396
X-RAY DIFFRACTIONf_dihedral_angle_d16.38432789
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.693744490925
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.662222147987
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.460312800531
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.01833621931
ens_2d_3BBX-RAY DIFFRACTIONTorsion NCS0.924927826132
ens_2d_4BBX-RAY DIFFRACTIONTorsion NCS0.540537020466
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.44331220.38723297X-RAY DIFFRACTION94.66
2.41-2.470.40081600.3543419X-RAY DIFFRACTION98.89
2.47-2.550.37571420.34463459X-RAY DIFFRACTION98.44
2.55-2.630.41221320.34313382X-RAY DIFFRACTION96.62
2.63-2.720.44041370.33173456X-RAY DIFFRACTION99.14
2.72-2.830.31991450.28113429X-RAY DIFFRACTION99.11
2.83-2.960.27661470.23153490X-RAY DIFFRACTION98.8
2.96-3.120.28871430.22553436X-RAY DIFFRACTION98.92
3.12-3.310.29761490.23463458X-RAY DIFFRACTION98.74
3.31-3.570.27081340.20043449X-RAY DIFFRACTION98.25
3.57-3.930.23461340.18793406X-RAY DIFFRACTION96.27
3.93-4.50.19861480.16173424X-RAY DIFFRACTION97.65
4.5-5.660.17891330.14823482X-RAY DIFFRACTION97.15
5.66-74.810.18441510.15953532X-RAY DIFFRACTION96.44
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.188725085317-0.28816345010.04063243743220.543718925991-0.0723651898529-0.005235401115090.0578717415629-0.154439146404-0.0468001535339-0.2701308435910.136189488267-0.525314693474-0.5602163930210.806334979599-0.000180790266860.5894171166830.03850345529120.04378533319460.6352513151420.006316720090970.52105984560219.377357565811.748831304513.5424924593
21.245958530270.962643867879-0.3746749814731.26947019799-1.294071678030.6312333657180.09170332765260.1546598070510.225875000988-0.00555073832558-0.08548019826580.0448996179769.81515937236E-50.4062718350267.75251488026E-50.5837170720410.0613593077256-0.008670421246070.5982537173560.05191072624230.55954144402211.503946599720.249639117813.0387641532
30.4905297485160.221663794405-0.2284797702180.695996795493-0.5785262327620.2416819825550.0357141586861-0.02561445734250.1570085374250.03169261603890.0578341546-0.0686546122691-0.2051862702470.2961838718522.70683091999E-50.5519495375190.0150891694474-0.01246381578480.6263812931640.06896426609290.4724472956512.30293422818.963410348415.1770128459
4-0.0558107957402-0.03465554583030.0455314504829-0.00703793853678-0.2795524419940.4278901041410.1867694577860.5957367968040.185846739833-0.01829202931360.295814512017-0.30931660689-0.492245800990.473361489350.003918547375260.5173039190220.002602311445150.04337101530640.7739741713940.09099242976560.41014066411820.206462490820.92778736453.23381826086
50.011105785360.0849036873601-0.08088320211740.0309331247605-0.1518605835350.1159739718580.0464145424611-0.216416768480.558724653261-0.4193448329960.1493259714540.283465692405-0.3117332794610.0179367301399-0.0004585027959380.8702402710.1084405507870.04378231119050.9223537343440.1845636404530.864588263290.75765662049126.3203456018-3.91418695813
62.233327074140.708952386319-0.8840716529741.27663899880.7181878213641.279177488380.1802523945860.1139250577880.06711554458540.0667676671944-0.0157575609120.3867144283880.00183267115102-0.0147332251375-5.88171960855E-50.4946667153110.03196905283190.03374752814150.4428348668930.03125295686070.52345984950.19193855132714.640598304119.8128976757
70.612106125348-0.1403022169610.1658421063870.08478003863350.06194283685820.232235724610.0372597414835-0.6847906461010.218327127578-0.253282835236-0.0806687738575-0.306452384360.0406510780462-0.060701336175-0.0002674618655570.616670532957-0.04975456378940.04078634670770.665883874185-0.1128454618960.701886028531-9.2019846170313.894214609724.9064501979
80.172389088497-0.138976603402-0.02627401106840.4108339432410.4163700472940.2844130759330.151413274855-0.274127873246-0.135455051585-0.322170184616-0.004951502332630.7784559678850.104527132026-0.03664702078320.0002351667592360.614251846923-0.02771151460210.05128219956220.6101331580630.009681658323950.628106593541-2.797714505667.2211067839228.6844684948
91.59516122540.427955889047-1.247038346161.03330795301-0.00424735306750.7854976122720.127718380214-0.151922554206-0.163134383055-0.1185348748840.2640643141510.3254733107340.254783363146-0.5160437954880.0001683727672540.5100055473950.03249337264960.004652764070330.498003136408-0.01691978073540.545542979415-2.8437333056410.735618203417.6061222724
100.122823673979-0.1989796499650.2638299524571.11840756906-0.9189990065980.7571656528460.0170081989491.28931769713-1.12946052697-0.0252224943112-0.0164794850860.130506603270.303209828015-0.440740457145-0.0002475522688450.6997135123010.0921360707909-0.02795449921930.669813528129-0.0380472211230.6527916405558.48002293853-0.98195937790517.265683077
110.141842322980.104683675561-0.02497133735790.05089658770220.003511907693990.1531700656730.957658506790.4275321208540.4583790734140.200504398514-0.340074632712-0.547109421268-0.01273733913641.102648625630.000576523457641.012601226820.18294693486-0.117620919780.6864878613050.01965844883410.92053086940211.2989988489-8.5310911058618.6873561982
120.28617157688-0.252091574546-0.02234501168650.147608834179-0.03764084265350.1858537075590.122049365005-1.39878103818-0.245000493196-0.172992846163-0.01397299930250.1633853648811.139781676350.791089810081-0.0003243133951560.9842011372260.158812124654-0.08840299372790.8016569704820.03970068428751.0371426021913.6639785203-3.3822899169127.3013018081
131.839680729620.5393660208790.3752467605281.823423233340.4702836396080.9106467977250.06703117671370.09152079088230.0164961123748-0.01175739126550.0518171604034-0.1243417523250.039916784861-0.110852905831-7.06088506927E-50.5256582220420.05125017994420.0103235666820.4483450352410.002587314989750.52312077851933.097856820217.984024497617.0559494233
140.06803655718530.1010431961670.136180829580.02325334765490.1654336867860.1368338874540.7912103474350.624199404711-0.808242482545-0.1805084963920.379566085788-0.981640343290.5556252981220.5572193862430.0007496256232870.8393865204460.15159597069-0.09137967653670.911964188019-0.0969704571231.0211463568247.69181918589.44085479494.77378388572
151.08631437882-0.222145457672-0.9900539038580.8188821308110.01028730754591.182584862370.0808188738671-0.07482834715480.0815935070024-0.104022648679-0.000936569999757-0.510340599022-0.1243866248250.2252285295972.25745946932E-50.4666523846410.0100798465384-0.03808462340290.466420952713-0.01016071422760.6654636563848.43588957726.488250997324.6919155755
161.299527101560.6072132883750.6083267712740.5798232182690.04070338814150.72821078178-0.001349358601790.18290410290.629226326068-0.02658298142870.201687122264-0.724899377372-0.01212811754980.3954316042256.06419729448E-50.553837009721-0.00477162420758-0.03075423474650.4181993392640.00135804549350.70658622121647.654090313130.968170974923.069423533
170.852114915389-0.206932492831-0.2699096482090.6281383110520.5288832495490.8375443844220.04825483996470.7355812111550.250285192407-0.274399011076-0.231994193943-0.320657521856-1.2682992963-0.1339781357040.02961264791591.035695794930.08958728732140.03572673309140.5220459054120.06800260284891.0032533740437.108201823839.648376189615.6209135628
180.1621306466760.00192831211982-0.186384341407-0.0176524259033-0.01744116227340.2495778028481.198092394480.9243577407110.902758655301-0.476982843035-0.2415846846060.607911500706-1.30682796446-0.5920478274380.005520594657811.297042562680.204414243803-0.08685882138270.6817890755190.1262014963931.1651095324932.436951173946.110982093114.9063628537
190.3404403912360.286881799030.4122459829130.3096763498950.3555051870020.516386910818-0.719153204199-0.519228837940.7879135499020.1908686256810.2086641237-0.463479871351-1.00993237935-0.61160049029-0.02311913518360.9838435716080.1565831224350.0764220993830.560400370464-0.0619880821761.1842070483629.309367088243.492106804124.2669957025
202.068791635-0.2947243309350.670351081931.75711838733-0.18972290361-0.06477621994880.110142704453-0.416835395625-0.106038683381-0.120488970806-0.239562601393-0.306257299465-0.244386426010.3585627502010.0003560611928440.612783107107-0.04986166759960.008591705358120.7387517847580.08201011017430.5839611802075.4705605650415.664057321456.4159510244
210.769653297774-0.774980120037-0.5118493391250.688810393780.4955240618530.337721807881-0.160261381035-0.535128868897-0.6478231832710.03982031549530.00144709749863-0.434279355594-0.0219864048377-0.102324007962-8.55979452239E-50.581477822761-0.0629569723867-0.04061719590060.9133243526760.2833785353520.7724981869769.24176914836.4714963359962.0269481725
220.0200341070071-0.05131201552250.08800982312920.08806442611-0.1144793241090.0455910535892-0.0954444477364-0.1865664587370.1226411505770.198046943208-0.1886960571970.234594121060.183881205807-0.4321021983294.48719140294E-50.667505804975-0.161231437704-0.04711104372841.23443789040.2565863249660.826020803158-8.484737421141.8500416629468.2178095558
232.167525420630.81881492394-0.2643508169141.183488241330.07321412846050.257118270607-0.0912975674894-0.3970032958710.477798158335-0.0791514187113-0.07772387797740.327475693669-0.0965806123356-0.4008495191526.10783246053E-50.6034394136830.0635296099742-0.0749536613670.659110221439-0.05299571654640.62563381237-8.1070260218525.301046598952.0421842741
241.77731666539-0.5407877915841.029179966990.7482182691330.1847428984590.844241439429-0.164031352652-1.495958524060.0746205416646-0.0577436850389-0.00646199803588-0.202136201185-0.265595852827-0.306722982043-0.01469999234750.6986414556480.0429810023154-0.03364154962040.772929711404-0.2109613633470.595608855237-8.0642171232524.568588501457.674074053
250.3761546834710.190621172307-0.4050534180.755530625149-0.4843238636490.4627298092180.419328290746-0.6558922525271.300369943770.301680943761-0.6609772941740.162808230257-1.42203735839-0.4661115940620.008229391282381.12426789852-0.006941718771950.07534391570360.881588958086-0.2019770152181.070705119713.3404466355934.174587621963.9471196833
260.118767060308-0.0357060081614-0.08827877237310.01355487079820.003066066926060.2303895081210.351475812774-1.051679094670.880050973278-0.0561461540139-0.479817916195-0.4538087783780.4424374743551.137544745730.002989693773591.5080300359-0.0192561503459-0.2389880015481.11952376212-0.1767717756671.354367309118.1133160611740.013574705366.3686548023
270.484436810060.007520636601160.03411142284090.20165622751-0.08937622765760.02681747947990.2042228810090.8389147666470.06808943523380.365577647392-0.842672814766-0.397280892557-0.897528463237-0.2706949160910.0001788441857341.38200338992-0.157428691672-0.01336054703090.724503878894-0.0818030718461.2401176460610.125303665939.459549779656.4068323668
281.391296821480.11063801013-0.7707062213590.3802562309770.1722895015860.620821750181-0.039423960001-0.740468389219-0.01279120839630.198859506725-0.09793274178120.3038447491150.099060196331-0.111718422741-0.00235286391840.675221028873-0.04477313458520.02990626113011.126480788150.01231579193640.5198402038625.216308027410.215729647865.6122086178
291.59545751709-0.533441329454-0.631822512752-0.5865512099680.1222795803270.199777718874-0.0746053222399-0.5523642226980.099081096688-0.0714692253585-0.06749931725050.119633764252-0.280968739742-0.3555640951250.0009179471447290.760939069201-0.04769680618860.008974365091290.81978500696-0.04050658161760.50794528242431.183629676914.100697141756.4342905743
300.444720137951-0.157992192951-0.07283510460880.04979038796490.08551873044590.1152065829190.223092062549-0.4964147862880.439418457839-0.06233886557520.285000926050.220329828861-0.7987187761990.1774835702050.0006010525150370.6103444907340.01588039716880.03225441659931.001211459460.03017461519310.54279652861321.93171915514.922956399759.9010290794
310.0195561064629-0.07445428468420.2584573110810.1323475520920.1813753858630.294035214970.138288807691-0.6883749177560.1517322984020.1841105279050.03990357705220.0416481757773-0.280073897333-0.2667458105120.0001419017217990.713360102676-0.111854226562-0.02716377553641.357911520530.1099966235490.59341570824428.710111505512.652461964475.0863651902
320.585513534136-0.1411638460660.1086946553060.7997929147010.1441335839080.04281532480520.0460590218083-0.389967587578-0.415542392807-0.3085499327110.2167559624070.08871156519880.5647184770410.142047227107-4.28334433032E-50.619300686262-0.02407380218730.01495370494420.887873103427-0.01054728732870.59330256262335.28819264137.1232084136650.3316424998
331.547060149810.2593584815420.7548504832210.526260295557-0.3156436824190.669475577593-0.0327203350438-0.5881211545450.3931329166730.002812246046820.101752661684-0.264980635387-0.03753798779560.3545398840621.1819385603E-50.566693423162-0.0406008108802-0.003623157117880.822780848268-0.06879077061040.58799415600346.220810844912.029010072154.3386002479
341.6416159705-1.37647551067-0.3270152312811.63591287509-0.2755515240170.3800598328460.0553320560178-0.436868093395-0.610188051091-0.133319476073-0.0526872512237-0.3740237639460.3577285150290.252557362594-0.0002393130115640.596025462002-0.01196458754270.01329484100320.8407251499120.07213423981260.63914827170442.97741681945.8846227686952.2880987775
350.3526242982740.0572741930140.3361186034480.5367861547410.4942119373570.6315553180460.7041614958470.0300512321766-1.49349509217-0.363727230405-0.2521101158410.1376465809971.270019796470.1915068945230.01218621352631.20482698121-0.0557572731869-6.45773005259E-50.9133724177610.09868103808920.96885248766532.7327589671-6.1111774436852.0016710857
360.0369532824930.08407321687080.0565115584060.07563395090470.1492492812750.1599014078730.1663943113780.442098774714-0.6239893632460.102139202298-0.1173006842060.2272021172930.760395211655-1.0525888025-0.0002203767795491.21132977709-0.171432364870.01477187828020.840520311506-0.03657910015161.1975219831827.8114552885-8.6408082093545.6080778909
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 43 through 54 )AA43 - 541 - 12
22chain 'A' and (resid 55 through 99 )AA55 - 9913 - 57
33chain 'A' and (resid 100 through 137 )AA100 - 13758 - 95
44chain 'A' and (resid 138 through 148 )AA138 - 14896 - 106
55chain 'A' and (resid 149 through 163 )AA149 - 163107 - 121
66chain 'A' and (resid 164 through 195 )AA164 - 195122 - 153
77chain 'A' and (resid 196 through 212 )AA196 - 212154 - 170
88chain 'A' and (resid 213 through 224 )AA213 - 224171 - 182
99chain 'A' and (resid 225 through 250 )AA225 - 250183 - 208
1010chain 'B' and (resid 62 through 83 )BB62 - 831 - 22
1111chain 'B' and (resid 84 through 98 )BB84 - 9823 - 37
1212chain 'B' and (resid 99 through 113 )BB99 - 11338 - 52
1313chain 'C' and (resid 43 through 148 )CC43 - 1481 - 106
1414chain 'C' and (resid 149 through 163 )CC149 - 163107 - 118
1515chain 'C' and (resid 164 through 212 )CC164 - 212119 - 167
1616chain 'C' and (resid 213 through 250 )CC213 - 250168 - 205
1717chain 'D' and (resid 59 through 83 )DD59 - 831 - 25
1818chain 'D' and (resid 84 through 98 )DD84 - 9826 - 40
1919chain 'D' and (resid 99 through 113 )DD99 - 11341 - 55
2020chain 'E' and (resid 43 through 117 )EE43 - 1171 - 75
2121chain 'E' and (resid 118 through 148 )EE118 - 14876 - 106
2222chain 'E' and (resid 149 through 163 )EE149 - 163107 - 118
2323chain 'E' and (resid 164 through 224 )EE164 - 224119 - 179
2424chain 'E' and (resid 225 through 250 )EE225 - 250180 - 205
2525chain 'F' and (resid 59 through 83 )FF59 - 831 - 25
2626chain 'F' and (resid 84 through 98 )FF84 - 9826 - 40
2727chain 'F' and (resid 99 through 112 )FF99 - 11241 - 54
2828chain 'G' and (resid 43 through 88 )GG43 - 881 - 46
2929chain 'G' and (resid 89 through 125 )GG89 - 12547 - 83
3030chain 'G' and (resid 126 through 137 )GG126 - 13784 - 95
3131chain 'G' and (resid 138 through 163 )GG138 - 16396 - 118
3232chain 'G' and (resid 164 through 178 )GG164 - 178119 - 133
3333chain 'G' and (resid 179 through 212 )GG179 - 212134 - 167
3434chain 'G' and (resid 213 through 249 )GG213 - 249168 - 204
3535chain 'H' and (resid 59 through 83 )HH59 - 831 - 25
3636chain 'H' and (resid 84 through 112 )HH84 - 11226 - 54

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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://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