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- PDB-8v8h: PI3Ka H1047R co-crystal structure with inhibitor in cryptic pocke... -

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基本情報

登録情報
データベース: PDB / ID: 8v8h
タイトルPI3Ka H1047R co-crystal structure with inhibitor in cryptic pocket near H1047R (compound 4).
要素
  • Phosphatidylinositol 3-kinase regulatory subunit alpha
  • Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
キーワードSIGNALING PROTEIN / H1047R / PI3K / PI3Ka
機能・相同性
機能・相同性情報


perinuclear endoplasmic reticulum membrane / response to muscle inactivity / negative regulation of actin filament depolymerization / regulation of toll-like receptor 4 signaling pathway / response to L-leucine / phosphatidylinositol kinase activity / regulation of actin filament organization / phosphatidylinositol 3-kinase regulator activity / response to butyrate / positive regulation of focal adhesion disassembly ...perinuclear endoplasmic reticulum membrane / response to muscle inactivity / negative regulation of actin filament depolymerization / regulation of toll-like receptor 4 signaling pathway / response to L-leucine / phosphatidylinositol kinase activity / regulation of actin filament organization / phosphatidylinositol 3-kinase regulator activity / response to butyrate / positive regulation of focal adhesion disassembly / autosome genomic imprinting / IRS-mediated signalling / cellular response to hydrostatic pressure / phosphatidylinositol 3-kinase activator activity / interleukin-18-mediated signaling pathway / PI3K events in ERBB4 signaling / myeloid leukocyte migration / 1-phosphatidylinositol-3-kinase regulator activity / phosphatidylinositol 3-kinase regulatory subunit binding / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / positive regulation of protein localization to membrane / Activated NTRK3 signals through PI3K / cis-Golgi network / ErbB-3 class receptor binding / negative regulation of fibroblast apoptotic process / cardiac muscle cell contraction / RHOF GTPase cycle / kinase activator activity / phosphatidylinositol 3-kinase complex, class IB / vasculature development / transmembrane receptor protein tyrosine kinase adaptor activity / RHOD GTPase cycle / Signaling by cytosolic FGFR1 fusion mutants / regulation of cellular respiration / positive regulation of endoplasmic reticulum unfolded protein response / enzyme-substrate adaptor activity / phosphatidylinositol 3-kinase complex, class IA / anoikis / phosphatidylinositol 3-kinase complex / Nephrin family interactions / RND1 GTPase cycle / Costimulation by the CD28 family / relaxation of cardiac muscle / positive regulation of leukocyte migration / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / MET activates PI3K/AKT signaling / RND2 GTPase cycle / PI3K/AKT activation / positive regulation of filopodium assembly / RND3 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / vascular endothelial growth factor signaling pathway / negative regulation of stress fiber assembly / growth hormone receptor signaling pathway / phosphatidylinositol 3-kinase / insulin binding / phosphatidylinositol-3-phosphate biosynthetic process / RHOV GTPase cycle / 1-phosphatidylinositol-3-kinase activity / negative regulation of cell-matrix adhesion / Signaling by ALK / RHOB GTPase cycle / negative regulation of macroautophagy / GP1b-IX-V activation signalling / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR2 / response to dexamethasone / RHOJ GTPase cycle / PI-3K cascade:FGFR4 / protein kinase activator activity / RHOC GTPase cycle / PI-3K cascade:FGFR1 / negative regulation of osteoclast differentiation / intracellular glucose homeostasis / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / CDC42 GTPase cycle / RHOU GTPase cycle / PI3K events in ERBB2 signaling / negative regulation of anoikis / T cell differentiation / RET signaling / intercalated disc / regulation of multicellular organism growth / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / RHOG GTPase cycle / extrinsic apoptotic signaling pathway via death domain receptors / PI3K Cascade / RHOA GTPase cycle / positive regulation of TOR signaling / endothelial cell migration / RAC2 GTPase cycle / RAC3 GTPase cycle / Role of phospholipids in phagocytosis
類似検索 - 分子機能
PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain ...PI3Kalpha, catalytic domain / Phosphatidylinositol 3-kinase regulatory subunit alpha, SH3 domain / PIK3R1, inter-SH2 domain / PI3K p85 subunit, C-terminal SH2 domain / PI3K regulatory subunit p85-related , inter-SH2 domain / PI3K p85 subunit, N-terminal SH2 domain / Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / Phosphoinositide 3-kinase C2 / Phosphoinositide 3-kinase, region postulated to contain C2 domain / C2 phosphatidylinositol 3-kinase-type domain / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Rho GTPase activation protein / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / C2 domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
: / : / Phosphatidylinositol 3-kinase regulatory subunit alpha / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.58 Å
データ登録者Gunn, R.J. / Lawson, J.D.
資金援助 米国, 1件
組織認可番号国
Not funded 米国
引用ジャーナル: J.Med.Chem. / 年: 2024
タイトル: Discovery of Pyridopyrimidinones that Selectively Inhibit the H1047R PI3K alpha Mutant Protein.
著者: Ketcham, J.M. / Harwood, S.J. / Aranda, R. / Aloiau, A.N. / Bobek, B.M. / Briere, D.M. / Burns, A.C. / Caddell Haatveit, K. / Calinisan, A. / Clarine, J. / Elliott, A. / Engstrom, L.D. / ...著者: Ketcham, J.M. / Harwood, S.J. / Aranda, R. / Aloiau, A.N. / Bobek, B.M. / Briere, D.M. / Burns, A.C. / Caddell Haatveit, K. / Calinisan, A. / Clarine, J. / Elliott, A. / Engstrom, L.D. / Gunn, R.J. / Ivetac, A. / Jones, B. / Kuehler, J. / Lawson, J.D. / Nguyen, N. / Parker, C. / Pearson, K.E. / Rahbaek, L. / Saechao, B. / Wang, X. / Waters, A. / Waters, L. / Watkins, A.H. / Olson, P. / Smith, C.R. / Christensen, J.G. / Marx, M.A.
履歴
登録2023年12月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年3月20日Provider: repository / タイプ: Initial release
改定 1.12024年3月27日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22024年4月10日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
D: Phosphatidylinositol 3-kinase regulatory subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)318,6398
ポリマ－316,9554
非ポリマー1,6844
水00
1
A: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
B: Phosphatidylinositol 3-kinase regulatory subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)159,3194
ポリマ－158,4772
非ポリマー8422
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-14 kcal/mol
Surface area59670 Å2
手法PISA
2
C: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
D: Phosphatidylinositol 3-kinase regulatory subunit alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)159,3194
ポリマ－158,4772
非ポリマー8422
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-17 kcal/mol
Surface area59110 Å2
手法PISA
単位格子
Length a, b, c (Å)233.850, 157.770, 121.900
Angle α, β, γ (deg.)90.000, 112.660, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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 2 through 409 or resid 416...
d_2ens_1(chain "C" and (resid 2 through 409 or resid 416...
d_1ens_2(chain "B" and (resid 326 through 331 or resid 333...
d_2ens_2(chain "D" and (resid 326 through 331 or resid 333...

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_1PROPROVALVALAA2 - 4096 - 413
d_12ens_1LYSLYSARGARGAA416 - 524420 - 528
d_13ens_1ASNASNLEULEUAA526 - 866530 - 870
d_14ens_1GLYGLYGLYGLYAA868 - 887872 - 891
d_15ens_1ILEILEASPASPAA889 - 939893 - 943
d_16ens_1GLUGLUGLUGLUAA950954
d_17ens_1VALVALTHRTHRAA952 - 974956 - 978
d_18ens_1GLUGLUMETMETAA976 - 1040980 - 1044
d_19ens_1GLNGLNALAALAAA1042 - 10461046 - 1050
d_110ens_1GLYGLYLYSLYSAA1049 - 10541053 - 1058
d_111ens_1ASPASPGLNGLNAA1056 - 10641060 - 1068
d_21ens_1PROPROVALVALCC2 - 4096 - 413
d_22ens_1LYSLYSARGARGCC416 - 524420 - 528
d_23ens_1ASNASNLEULEUCC526 - 866530 - 870
d_24ens_1GLYGLYGLYGLYCC868 - 887872 - 891
d_25ens_1ILEILEASPASPCC889 - 939893 - 943
d_26ens_1GLUGLUGLUGLUCC950954
d_27ens_1VALVALTHRTHRCC952 - 974956 - 978
d_28ens_1GLUGLUMETMETCC976 - 1040980 - 1044
d_29ens_1GLNGLNALAALACC1042 - 10461046 - 1050
d_210ens_1GLYGLYLYSLYSCC1049 - 10541053 - 1058
d_211ens_1ASPASPGLNGLNCC1056 - 10641060 - 1068
d_11ens_2METMETALAALABB326 - 3315 - 10
d_12ens_2TRPTRPSERSERBB333 - 39312 - 72
d_13ens_2PROPROILEILEBB395 - 53974 - 218
d_14ens_2SERSERARGARGBB541 - 577220 - 256
d_15ens_2TRPTRPTRPTRPBB583262
d_21ens_2METMETALAALADD326 - 3315 - 10
d_22ens_2TRPTRPSERSERDD333 - 39312 - 72
d_23ens_2PROPROILEILEDD395 - 53974 - 218
d_24ens_2SERSERARGARGDD541 - 577220 - 256
d_25ens_2TRPTRPTRPTRPDD583262

NCSアンサンブル:
ID
ens_1
ens_2

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要素

#1: タンパク質 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform


分子量: 124810.422 Da / 分子数: 2 / 変異: H1047R / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PIK3CA / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P42336
#2: タンパク質 Phosphatidylinositol 3-kinase regulatory subunit alpha / PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit ...PtdIns-3-kinase regulatory subunit alpha / Phosphatidylinositol 3-kinase 85 kDa regulatory subunit alpha / PtdIns-3-kinase regulatory subunit p85-alpha


分子量: 33666.961 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PIK3R1, GRB1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P27986
#3: 化合物 ChemComp-YO4 / 2-({(1R)-1-[2-(4,4-dimethylpiperidin-1-yl)-3,6-dimethyl-4-oxo-4H-1-benzopyran-8-yl]ethyl}amino)benzoic acid


分子量: 448.554 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C27H32N2O4 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物 ChemComp-YNZ / (2S)-N~1~-[(4P)-2-tert-butyl-4'-methyl[4,5'-bi-1,3-thiazol]-2'-yl]pyrrolidine-1,2-dicarboxamide


分子量: 393.527 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C17H23N5O2S2 / タイプ: SUBJECT OF INVESTIGATION
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: 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: 3.27 Å3/Da / 溶媒含有率: 62.43 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.2 M Sodium acetate, 0.1 M Sodium citrate pH 5.5, 4% w/v PEG 4000.

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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: CLSI / ビームライン: 08ID-1 / 波長: 0.95371 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2022年8月12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: 0.95371 Å / 相対比: 1
反射解像度: 3.58→48.21 Å / Num. obs: 47973 / % possible obs: 99.54 % / 冗長度: 4.6 % / Biso Wilson estimate: 104.01 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.08 / Net I/σ(I): 9.1
反射 シェル解像度: 3.58→3.71 Å / Num. unique obs: 4774 / CC1/2: 0.75 / Rpim(I) all: 0.4

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解析

ソフトウェア名称: PHENIX / バージョン: 1.20.1_4487 / 分類: 精密化
精密化構造決定の手法: 分子置換 / 解像度: 3.58→48.21 Å / SU ML: 0.4945 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 30.4375
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.2719 2353 4.91 %RANDOM
Rwork0.222 45565 --
obs0.2244 47918 99.54 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 143.7 Å2
精密化ステップサイクル: LAST / 解像度: 3.58→48.21 Å
タンパク質核酸リガンド溶媒全体
原子数20726 0 118 0 20844
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00421295
X-RAY DIFFRACTIONf_angle_d0.770828732
X-RAY DIFFRACTIONf_chiral_restr0.04593093
X-RAY DIFFRACTIONf_plane_restr0.00543670
X-RAY DIFFRACTIONf_dihedral_angle_d15.53828161
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.830597485796
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.16134251677
LS精密化 シェル解像度: 3.58→3.85 Å
Rfactor反射数%反射
Rfree0.3869 128 -
Rwork0.3421 2643 -
obs--99.64 %
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)
11.71144971866-0.5187769470070.4953987429691.6974084826-0.3082854407011.44115704918-0.08705707548130.100349177026-0.150098475436-0.103790818319-0.02484219294860.2001279373050.09690336996470.1087996302680.1000311686160.972827536151-0.0257453821635-0.003419502376670.8111735596060.02615129234690.80303992391332.22663721230.022304662913.6228749582
20.717698874562-0.1939137387370.4944566785251.28867849833-0.3338249484472.23385587364-0.0224652295804-0.313519255783-0.1562230678960.209265928137-0.01160989218970.2407644634530.0939998690521-0.2007207905050.06483249668971.12690206954-0.02541817064810.2380922264210.975600586280.04886783112680.89277943158632.9738133639-4.8830176462739.4541344912
30.969228356124-0.117034205845-0.1076094210461.28365773070.3737623088382.217165527070.01091567121590.291094680298-0.206170404837-0.309919201453-0.06575484288730.4988075214890.0464317435745-0.04639308462240.05256545466191.09610285933-0.00261855606099-0.1687731115930.85291764217-0.1092057890930.99375704777826.4189658225-15.76393466440.0428082031735
41.614989258920.06344507544280.07698832111531.57041953020.1733969963871.020650378360.044540887952-0.0627076084704-0.214735229072-0.139864961103-0.0410515317688-0.1075814622640.2770768663650.238621181281-0.005902384717911.023831353950.120262269660.04733783671010.8044926871580.03426819823970.7259212094351.7156924977-7.772616427517.7421043921
50.8768741701380.0309099833221-0.3994003927010.0008952077954770.08322686829441.14093743981-0.1285345932680.662229760718-0.545868752156-1.2452784035-0.444332268146-0.433017616049-0.28536970164-0.3435295267210.5067330357813.12815614280.2977847676250.2405204297252.25920742017-0.09185194298692.6610882838941.8341820976-38.0255756127-12.8954305211
60.38060105566-0.836273741782-0.8245472461441.471661626071.144244789780.3731083215120.3429249016270.1084585911480.0619489105872-1.06323776777-0.118360717958-0.323467091173-0.3046006057140.0640013757533-0.1812168946771.653468788050.1375217939160.04955803967751.1247572556-0.1152539889591.311147492940.626931142215.1267500932-8.91748203748
71.75127531774-0.155169759895-0.1081257914451.69325315740.5133532591961.47807259645-0.140853213402-0.126183951681-0.1958160623420.06891793483660.406722041938-0.9277480517310.1785256377860.389043017217-0.2362069899260.7293670254190.0795391287967-0.07542680095261.05937912401-0.2538554006381.3651246493363.6237421207-29.404392023991.224501874
81.663978927460.0562140219012-1.033161303851.728429925270.7876662083481.952802176950.169014528478-0.3397208424520.0347347478210.250815943790.0546486363398-0.0856723090111-0.4877886245610.265590637901-0.1871438733060.9851323339460.01540347137520.0002342608349410.963825464972-0.03795099004980.78399108110641.43954479724.30749258805108.845909892
91.285775516610.2392527537680.05299563513741.1718506881-0.170468626207-0.00223098536857-0.449716301961-0.0376909856513-0.324235153022-0.3292235148080.283100041328-0.567017336066-0.1529331357550.2104916540690.224786261831.1314486902-0.2124601744910.2340755213021.1631216623-0.1919941855941.3008980057364.51166630244.9799111155593.3414340229
100.792950851104-0.5682548245420.1705292549091.04362156078-0.8188471130790.8216427079260.551893232146-0.162487222725-0.0143614627459-0.963823657211-0.701044894584-1.06772228657-0.3186070719490.5388909599280.4743091235451.80419785432-0.7059987763180.7585136223072.11725586223-0.3121420715212.3277108240884.988124343416.582320628472.3677000584
110.878106366601-0.541612564495-0.01373325774731.90040124946-0.106367007771.3550390881-0.1555578803420.05423396138120.142532861996-0.5816709099230.389513646305-0.680541527315-0.7124059483040.573631066265-0.173764710231.6668409847-0.4186407041920.3999838682911.4754860813-0.1721409108731.7968497122374.999239527922.30846725284.489331611
121.212015363920.5638585388090.3834622353661.522949022830.4192027797091.562748719960.06118727912090.09488919696520.101037719602-0.4363719359720.177550574624-0.444449196592-0.4724541397620.328972053212-0.228352345480.929517440782-0.1450886331120.225746051990.835719667231-0.0801098749830.85894761971351.6621581551.5480919037388.212111211
134.388055552610.0414737210908-0.4339944376632.33828573201-0.2633958825112.870228552880.3561089212361.14552042368-0.0203499961304-0.00918499104227-0.0976297936732-0.0509121741755-0.702470063334-1.06561149562-0.2182649392121.312074899190.2480564479530.1890271744891.13357681170.1830093289720.77405115640429.740781813410.302597511772.3565244318
140.623793341030.5727548297730.3080654426661.66082639057-0.05072913683241.84401206718-0.2596531601610.5500234270330.283661532857-0.625321882890.131455867727-0.0215341215579-1.331391231880.1189958622020.07845038558162.11499215741-0.09965643583390.3900820648990.977327969410.0727119639571.1276496459439.923410241522.100724067372.1969017688
150.01246432185180.0188729876185-0.01744726761410.00117672823899-0.005674612256880.006420823795580.6596629605840.6494939246790.1942146394580.0752460314198-0.2616434293760.288242084875-0.6022194189970.308260481159-0.3121176438353.112057652310.1180243284850.1810583649232.580402536620.3793036570313.0879604463369.304664977539.062469997265.4237513988
160.5692636523610.3022462525420.2583896914230.9053358038020.4006152731641.20092497148-0.1721799333510.257014544470.110329274625-1.388092430430.0340540636458-0.6927418704790.07934030870660.4242981280850.1095189077061.5586668268-0.09721742108110.2629458931591.70784103751-0.2438303906351.6095810136771.9311728931-13.199060364168.4384346461
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 2 through 121 )AA2 - 1211 - 120
22chain 'A' and (resid 122 through 264 )AA122 - 264121 - 263
33chain 'A' and (resid 265 through 602 )AA265 - 602264 - 558
44chain 'A' and (resid 603 through 1064 )AA603 - 1064559 - 1020
55chain 'B' and (resid 326 through 428 )BC326 - 4281 - 89
66chain 'B' and (resid 429 through 587 )BC429 - 58790 - 239
77chain 'C' and (resid 2 through 121 )CD2 - 1211 - 120
88chain 'C' and (resid 122 through 270 )CD122 - 270121 - 269
99chain 'C' and (resid 271 through 354 )CD271 - 354270 - 340
1010chain 'C' and (resid 355 through 418 )CD355 - 418341 - 399
1111chain 'C' and (resid 419 through 576 )CD419 - 576400 - 532
1212chain 'C' and (resid 577 through 853 )CD577 - 853533 - 809
1313chain 'C' and (resid 854 through 963 )CD854 - 963810 - 911
1414chain 'C' and (resid 964 through 1064 )CD964 - 1064912 - 1012
1515chain 'D' and (resid 326 through 428 )DF326 - 4281 - 89
1616chain 'D' and (resid 429 through 587 )DF429 - 58790 - 239

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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