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- PDB-8tbh: Tricomplex of RMC-7977, KRAS G12R, and CypA -

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基本情報

登録情報
データベース: PDB / ID: 8tbh
タイトルTricomplex of RMC-7977, KRAS G12R, and CypA
要素
  • GTPase KRas
  • Peptidyl-prolyl cis-trans isomerase A
キーワードHYDROLASE/INHIBITOR / inhibitor / complex / small GTPase / cancer / tricomplex / HYDROLASE-INHIBITOR complex
機能・相同性
機能・相同性情報


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / protein peptidyl-prolyl isomerization / Basigin interactions / forebrain astrocyte development / cyclosporin A binding / negative regulation of epithelial cell differentiation / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / Early Phase of HIV Life Cycle / Integration of provirus / negative regulation of protein phosphorylation / APOBEC3G mediated resistance to HIV-1 infection / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / viral release from host cell / skeletal muscle cell differentiation / RAS signaling downstream of NF1 loss-of-function variants / Calcineurin activates NFAT / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / activation of protein kinase B activity / Signalling to RAS / Binding and entry of HIV virion / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / positive regulation of viral genome replication / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / negative regulation of protein kinase activity / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / protein-membrane adaptor activity / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / positive regulation of glial cell proliferation / GRB2 events in EGFR signaling / neutrophil chemotaxis / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / homeostasis of number of cells within a tissue / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / positive regulation of protein secretion / peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase / FCERI mediated MAPK activation / RAF activation
類似検索 - 分子機能
Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / GTPase KRas / Peptidyl-prolyl cis-trans isomerase A
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: 1.5 Å
データ登録者Bar Ziv, T. / Zhang, D. / Tomlinson, A.C.A. / Knox, J.E. / Yano, J.K.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Nature / 年: 2024
タイトル: Concurrent inhibition of oncogenic and wild-type RAS-GTP for cancer therapy.
著者: Holderfield, M. / Lee, B.J. / Jiang, J. / Tomlinson, A. / Seamon, K.J. / Mira, A. / Patrucco, E. / Goodhart, G. / Dilly, J. / Gindin, Y. / Dinglasan, N. / Wang, Y. / Lai, L.P. / Cai, S. / ...著者: Holderfield, M. / Lee, B.J. / Jiang, J. / Tomlinson, A. / Seamon, K.J. / Mira, A. / Patrucco, E. / Goodhart, G. / Dilly, J. / Gindin, Y. / Dinglasan, N. / Wang, Y. / Lai, L.P. / Cai, S. / Jiang, L. / Nasholm, N. / Shifrin, N. / Blaj, C. / Shah, H. / Evans, J.W. / Montazer, N. / Lai, O. / Shi, J. / Ahler, E. / Quintana, E. / Chang, S. / Salvador, A. / Marquez, A. / Cregg, J. / Liu, Y. / Milin, A. / Chen, A. / Ziv, T.B. / Parsons, D. / Knox, J.E. / Klomp, J.E. / Roth, J. / Rees, M. / Ronan, M. / Cuevas-Navarro, A. / Hu, F. / Lito, P. / Santamaria, D. / Aguirre, A.J. / Waters, A.M. / Der, C.J. / Ambrogio, C. / Wang, Z. / Gill, A.L. / Koltun, E.S. / Smith, J.A.M. / Wildes, D. / Singh, M.
履歴
登録2023年6月28日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年2月7日Provider: repository / タイプ: Initial release
改定 1.12024年4月24日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年6月5日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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: GTPase KRas
B: GTPase KRas
C: Peptidyl-prolyl cis-trans isomerase A
D: Peptidyl-prolyl cis-trans isomerase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,98810
ポリマ－75,1654
非ポリマー2,8236
水10,593588
1
A: GTPase KRas
D: Peptidyl-prolyl cis-trans isomerase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)38,9945
ポリマ－37,5832
非ポリマー1,4123
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: GTPase KRas
C: Peptidyl-prolyl cis-trans isomerase A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)38,9945
ポリマ－37,5832
非ポリマー1,4123
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)66.418, 85.673, 127.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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要素

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タンパク質 , 2種, 4分子 ABCD

#1: タンパク質 GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


分子量: 19458.979 Da / 分子数: 2 / 変異: G12R / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KRAS, KRAS2, RASK2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01116, small monomeric GTPase
#2: タンパク質 Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


分子量: 18123.582 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: PPIA, CYPA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62937, peptidylprolyl isomerase

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非ポリマー , 4種, 594分子

#3: 化合物 ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Gpp(NH)p


分子量: 522.196 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H17N6O13P3
コメント: GppNHp, GMPPNP, エネルギー貯蔵分子類似体*YM
#4: 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: 2 / 由来タイプ: 合成 / 式: Mg
#5: 化合物 ChemComp-ZNI / (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide / RMC-7977


分子量: 865.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C47H60N8O6S / タイプ: SUBJECT OF INVESTIGATION
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 588 / 由来タイプ: 天然 / 式: H2O

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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: 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: 2.35 Å3/Da / 溶媒含有率: 47.57 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 17% PEG4000, 0.1 M imidazole, pH 8.0

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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: 0.95375 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2023年6月16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: 0.95375 Å / 相対比: 1
反射解像度: 1.5→63.77 Å / Num. obs: 116906 / % possible obs: 99.75 % / 冗長度: 7.3 % / Biso Wilson estimate: 22.21 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1048 / Rpim(I) all: 0.04139 / Rrim(I) all: 0.1129 / Net I/σ(I): 7.51
反射 シェル解像度: 1.5→1.554 Å / 冗長度: 7.5 % / Rmerge(I) obs: 2.692 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 11564 / CC1/2: 0.37 / CC star: 0.735 / Rpim(I) all: 1.035 / Rrim(I) all: 2.888 / % possible all: 99.25

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
PHASER位相決定
HKL-2000データ削減
Aimlessデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 1.5→63.77 Å / SU ML: 0.2456 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 27.7011
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2251 5937 5.09 %
Rwork0.1959 110773 -
obs0.1974 116710 99.68 %
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: 35.51 Å2
精密化ステップサイクル: LAST / 解像度: 1.5→63.77 Å
タンパク質核酸リガンド溶媒全体
原子数5290 0 124 588 6002
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00565564
X-RAY DIFFRACTIONf_angle_d0.80927533
X-RAY DIFFRACTIONf_chiral_restr0.0753808
X-RAY DIFFRACTIONf_plane_restr0.0052967
X-RAY DIFFRACTIONf_dihedral_angle_d13.36132135
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.42292220.38933529X-RAY DIFFRACTION96.85
1.52-1.530.34161780.36473655X-RAY DIFFRACTION99.3
1.53-1.550.37881880.35533652X-RAY DIFFRACTION99.43
1.55-1.570.37232020.34443639X-RAY DIFFRACTION99.53
1.57-1.590.34522020.32763644X-RAY DIFFRACTION99.61
1.59-1.620.30921930.30673664X-RAY DIFFRACTION99.66
1.62-1.640.31951900.30073634X-RAY DIFFRACTION99.74
1.64-1.660.40022090.30933671X-RAY DIFFRACTION99.77
1.66-1.690.35411950.29173658X-RAY DIFFRACTION99.79
1.69-1.720.30441620.27253671X-RAY DIFFRACTION99.61
1.72-1.750.26531900.25383707X-RAY DIFFRACTION99.64
1.75-1.780.28511950.24343650X-RAY DIFFRACTION99.77
1.78-1.810.28891730.23863657X-RAY DIFFRACTION99.74
1.81-1.850.26651960.23293711X-RAY DIFFRACTION99.8
1.85-1.890.27761900.22213642X-RAY DIFFRACTION99.69
1.89-1.930.24121970.21563664X-RAY DIFFRACTION99.51
1.93-1.980.23691980.2063686X-RAY DIFFRACTION99.87
1.98-2.030.27111970.2133678X-RAY DIFFRACTION99.95
2.03-2.090.24631890.20963724X-RAY DIFFRACTION99.87
2.09-2.160.24691910.20133692X-RAY DIFFRACTION99.92
2.16-2.240.23282080.19713683X-RAY DIFFRACTION99.9
2.24-2.330.24052060.19723712X-RAY DIFFRACTION99.97
2.33-2.440.22411910.19483703X-RAY DIFFRACTION99.92
2.44-2.560.24292010.19633719X-RAY DIFFRACTION99.95
2.56-2.720.24342020.1973712X-RAY DIFFRACTION99.95
2.72-2.930.23462070.18683746X-RAY DIFFRACTION99.92
2.93-3.230.20142100.18273730X-RAY DIFFRACTION100
3.23-3.70.19952300.16893766X-RAY DIFFRACTION99.97
3.7-4.660.15662280.14333783X-RAY DIFFRACTION99.95
4.66-63.770.17891970.16183991X-RAY DIFFRACTION99.83
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)
13.862268291220.5980225229860.741013753373.024269686741.323541033484.07600024666-0.0348076962674-0.0651524500072-0.008066140592850.159943895108-0.0322992768087-0.2174263341990.02862167170720.1473104801290.0292045540410.168888378422-0.006859289051210.007114489111030.179237801340.04174579709740.130984976288-15.8856370157-9.619172077613.0929846835
23.494161057852.92456220933-2.975044727725.43490627426-0.3248524984554.00201458813-0.1214270174550.356430835157-0.548001219699-0.476229661708-0.22244293672-0.4977463251890.1517344010130.3788245946830.2898197779770.24800380050.05978365173390.03465137628840.3616354882810.02016265989730.196742891584-15.158838942-19.46061491014.52220767533
36.465486659463.151279463440.878435406494.90628636303-0.3007538979843.970476652490.202642113327-0.3472586274520.4015880995420.56662741316-0.363964339307-0.012439765926-0.2134703517830.42564825350.1123543657180.204777685946-0.0324461616005-0.01154283039140.303427295624-0.03813643913380.15611915529-11.7183589136-7.2218037830117.8362925488
47.034755748273.73254952966-0.455927689452.082450976411.565371009160.5769256764660.197263247799-0.2767324327370.1382343554810.217070518204-0.1746909829920.4119803366170.0281297812353-0.3545496921710.08247854685250.2471934116040.02225657507280.0003188967028270.2694702055960.05154763908630.201643035848-30.3114529371-15.118388666317.24271383
52.18681142497-0.151844161347-0.8190090065192.973587345980.9603031531116.37841269377-0.05771806617660.0177360752580.2563575015480.143560842721-0.0001582961460050.653900636671-0.258558827286-0.7483718577030.0661790148070.1888282577180.06224405120030.03496830645880.2854641673290.01003303800170.277568689449-29.273587929-4.5153356129810.6083424446
63.81727284313-0.464842510284-1.426515116192.780082581690.9688436411444.209844651220.1502269601220.7371906083160.496893541606-0.53188512953-0.09142510761360.172882805664-0.516455008815-0.431886012401-0.06985276356380.2991270400790.0419500247399-0.004060075292170.3403854029850.09019268267970.222554799885-22.4603871786-1.44528804448-0.369994823749
79.96700516129-3.08344227961-2.984243820649.26928072272.882896237562.05961797290.0790554406275-0.4618494805071.157439482110.1669441765660.0886853334296-0.0609822554777-0.9680041896030.254943447942-0.149871043360.358107560516-0.0378164904242-0.009809339727550.221578718216-0.03135940600990.290705145945-16.45265365282.9963770658415.9554620638
83.100516268322.861473010340.71409206384.908277189991.409284564752.027787634770.3792282216890.039328822841-0.2558911015070.697330646144-0.184285905717-0.5781871732610.0542791018674-0.0416926718197-0.216397812510.395856970669-0.0800416109225-0.0715316765240.2906254485550.04347266294190.189146180695-17.6292076289-27.728731920235.8578567705
90.5150816768-0.198115495192-0.6048755365640.06473703962410.2024904388320.6567342266130.184405773016-0.122626526427-1.076882100080.6089325181450.0381825669265-1.365417161820.554351079850.167463931578-0.267976194110.512467790702-0.0416690213521-0.2961906954270.361274463294-0.007222818835960.87411667997-4.9399612975-30.463468135935.8527811315
104.639466920194.06785329691-0.2602623419725.40894135343-0.475934188032.283670282150.03736842420250.1033563098440.01760073938310.264462471190.04491222036390.0850183523945-0.00890342059693-0.152682765431-0.1091595949960.260071772498-0.0278644931454-0.009334348787920.275438083425-0.002556103440280.159164471689-21.5946866052-28.299544076432.42768902
1110.00274970135.44851850659-1.228366930325.707319376171.620390942012.000281909070.235178286553-0.2456820310890.7366860151350.734440430052-0.102369596648-0.0960014862914-0.468969864570.441469088793-0.05308817614780.564284628982-0.00992066666894-0.09107219547880.3389369736940.01080696410460.336436135106-15.1737236336-11.803547712737.350334246
123.236486669241.285271591142.589322468162.941676421960.1385248277763.630293353860.73538261824-0.8676451192410.4183372916581.47701745725-0.723937463156-0.00867623737553-0.286517526763-0.2956608592680.131792377770.957002166625-0.260306434148-0.09157011209350.494490362147-0.02683711983540.209552732874-17.0214540963-18.201919875147.6045406818
131.364918410591.720096771631.652962877863.257446983520.6356280408413.809459875780.419832378939-0.7730162644860.8232672802711.1351939892-0.6007170547170.277792725641-0.340489992237-0.6903305929590.1260062668460.929256301356-0.2305884518980.07334100570960.579029491215-0.06982770663410.198609942518-24.6228176911-20.40838983646.4271990062
140.874226361754-1.26552318511.689253165061.83249312221-2.43240948913.23162530494-0.0443398059842-0.648289540804-0.4594577020940.9010249463730.3749463101630.1435372733770.264348498568-0.181052198076-0.3665004574111.53217986616-0.203936274538-0.8027859100130.6243116449190.3832275458660.683851563173-9.13292603798-32.379529518654.7506538346
152.49742475369-0.1817304706260.2291233659811.668004480121.583710825187.098070206870.169622947887-1.14586228619-0.3534833085230.973705517866-0.06118506353380.0667657398540.896938645698-0.547181321627-0.08477596110731.54878657254-0.6036308481710.2117196418841.13209001697-0.1294906035820.073609073379-22.0430016574-24.539389677457.798475876
164.81819326558-1.47936913275-1.504654630573.721016469590.898531631013.172266505180.62605242529-0.773474801785-0.5578402908481.37174581251-0.239236511083-0.6298948657860.630814632791-0.153888523955-0.2655783343851.19111686538-0.377651313764-0.4439627127920.404845227390.4412229057790.123879346089-17.0955355506-33.890223939147.0447867238
178.681550955320.1412208360131.326557919585.985427201080.06647725599966.434697955780.505763827858-0.836766811287-0.1743817178280.838067374468-0.4467001690750.5246121221210.0524413628617-0.960171708271-0.06264286577640.537364441071-0.194541274890.08273907836650.500510892766-0.004552727549440.222256516092-29.5883379153-28.701798873141.2349416195
185.901226604742.171463956572.825109174215.092161712442.827287026656.236769379690.1833046420550.469318005732-0.0227038805539-0.2543702244850.0134769295768-0.4471550552020.1807963923780.661756636073-0.14311200220.2326724607360.02855785111880.01255214458580.344285448188-0.02307817616730.217402261114.8447887698-16.292406455318.34770776
192.43243816714-0.1457700174280.7190814940842.915738811120.2513485066784.306574731030.04306223864430.183776485843-0.06510498261610.124387462794-0.00906967657151-0.4391292491680.1400316542790.371826355122-0.02340851778340.1661513903590.0110377787215-0.03566435460630.316815916047-0.03181042156540.23085955337817.2298410702-14.418577658125.3044856347
202.97651576489-1.07502786220.7471343621482.721654528970.08430842902161.741476217120.1447505585730.345857737408-0.1909270226530.0566084782263-0.0407861334832-0.22188814480.319437212330.105401031798-0.1398425444380.2627832666740.0206301062139-0.05096014739320.24158641117-0.03116564452940.1849963409687.31075226545-20.341871708825.0088014853
212.00700312648-1.37631275905-3.419872533094.713837123911.643843159735.545066295230.1319375365940.280651608639-1.10062163868-0.144844946423-0.1217060749130.1276220874560.730442297207-0.0461181324675-0.04481535512290.4255034821770.00320982416519-0.1298950927050.320400735233-0.07600766951860.427761979446.2754435215-28.459957857629.4285686966
225.2682698121-2.41738906927-1.517627284382.887190200813.956195745456.368017680940.197613498705-0.662938623041-0.5403230568670.9391602094060.0274523000081-0.3800413529840.810762862430.305540865135-0.1266805502030.4141177620590.0388390756936-0.1963448374650.3238128560880.0393328782850.41847511415815.6331406855-23.113980173137.738640494
233.195981344730.01026376258470.9552826807972.117776526610.09262238465652.127067460750.0227885454837-0.009960134438740.1392226300280.190295052568-0.048753397146-0.109496149358-0.04459617372280.08400990966410.02742741594290.226486106065-0.0341921509794-0.04799741587620.203226543108-0.01696699780810.1604510314517.3617239202-10.512178006633.417615736
242.83713588828-0.3615597508491.030651556473.475375909291.63564012444.743549861220.08249118958620.2608121626930.03013072669840.141876319903-0.0298930480122-0.189356924954-0.4152930664980.230470601145-0.02536879143720.219515679017-0.0130189772247-0.06958130392370.220476408988-0.006344540238270.18014404412510.58309486-8.3360373407229.0283956905
259.956860322196.59151372309-4.027467626629.06792906797-1.215857128863.87828550628-0.2707995956220.7268042336910.171647466327-0.3757803969890.2629252190320.339456341382-0.069040136245-0.544167313546-0.04447973483360.3246829684820.0309131929998-0.01188110971330.381869379624-0.001501568850510.1280679596112.25139663733-12.078782334315.4151260054
262.19706471852-0.671595431385-0.4557911932082.154026534080.5520128803592.891809697580.1687165869040.733739780977-0.452661067295-0.0761261710265-0.09926887119960.04102247324170.349742635915-0.191544449456-0.08008439743080.2642070056930.0236161801769-0.06189843879350.337778167861-0.07503920755680.1681184653444.02534507901-20.482659529919.6105001007
272.92833297458-1.289555165971.089891727592.28983812218-0.2872482932472.817068187770.209842451780.191001630966-0.4467691144630.00862500783015-0.0132587554306-0.1912822371980.5700099747230.230894355733-0.1905960103220.2651231563890.0611172899524-0.009552108367080.203475014258-0.01905081513980.177644560285-19.4598096026-47.877036285410.9350224546
282.58997904017-0.2064514422220.4249960506552.69013506566-0.8129555359623.460658908390.03064982334290.162139338787-0.236186151038-0.1822302068110.0428240508246-0.05114589817150.415176468361-0.009756789467460.002057516668470.2306988930280.0234253750608-0.03472465890590.167952879223-0.04200691190560.164921822059-25.4517520729-46.56895027626.2376367242
291.50116346575-0.17507347841-1.2232828931.736876277111.198169519173.394202997210.00058067542250.0509908378905-0.134235364128-0.06133618052410.000495544455286-0.1142728024470.09999161859390.183055161455-0.007113657415340.2054222953470.0429308493402-0.01132318900620.2569343799680.003012866635970.139005126106-19.1807799476-37.37943198149.0827775123
306.31393188294-0.559772145188-2.173032104522.007784896424.990188801954.622555601940.01172233523490.2376636769390.18542792859-0.070494623688-0.0314788859711-0.591135212486-0.26168101810.13825617897-0.0007216629887840.2632281184260.007212804682590.01002511957870.3137799897040.0005269555529430.218153016894-14.8375438671-32.22367197212.78761472786
314.19653778567-0.547662342027-0.24894575053.028586693490.005980705694366.79350647816-0.09306404993350.2703076104440.189338722031-0.2515907271920.0670119659518-0.0150389717965-0.02431629772780.3332017458550.0224929467390.2438746390790.0226388372607-0.009320946874990.322269668294-0.01819842505940.134456181604-24.9937071019-36.2281248156-4.92345863548
322.167235903480.4307367011660.8876306525791.2823268970.08734607719842.391054509620.0948993959733-0.032199521697-0.005539426552820.02972642035610.04720267325820.1225442978310.115914703207-0.11947537376-0.1042970348250.1652469430260.0141430455167-0.01602662397720.1917988176310.01246165030810.125560166992-31.9849463994-35.16505872228.88811813535
335.60840742478-1.527217414552.329273274222.56331595186-1.221533928715.759282782660.121576984554-0.0509822737517-0.456413368481-0.04759057736210.1661001606010.372570698920.428739372881-0.128969712899-0.2796011119530.16541502589-0.0221562765406-0.017638471380.1611193306730.0132059318840.115054622976-31.4051393077-41.634335442911.1016627712
345.73721802213.8405784586-0.4565840639178.194418527060.3868057071343.105369173140.164412845802-0.392298717701-0.09342117087350.222716047254-0.05465810966-0.1466413451810.1374520379980.0217148360657-0.06610189815640.2059898369250.0611976718032-0.06684515611220.2696989124380.05125745399330.194780846278-19.7309449286-40.73947327122.2681878882
351.8279494415-0.1520582278711.130195417836.517669114082.823879694673.873892072290.01157813635880.0831951278423-0.01306814041580.3388473950670.0371584911354-0.4303863871990.1642779402930.245533618891-0.1048729721520.1638958551880.0228996049672-0.01663195309250.2427659319930.01407776377750.120772050114-15.6124101997-37.741089766914.2412735985
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 58 )
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 116 )
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 151 )
7X-RAY DIFFRACTION7chain 'A' and (resid 152 through 169 )
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 25 )
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 36 )
10X-RAY DIFFRACTION10chain 'B' and (resid 37 through 61 )
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 74 )
12X-RAY DIFFRACTION12chain 'B' and (resid 75 through 104 )
13X-RAY DIFFRACTION13chain 'B' and (resid 105 through 116 )
14X-RAY DIFFRACTION14chain 'B' and (resid 117 through 126 )
15X-RAY DIFFRACTION15chain 'B' and (resid 127 through 137 )
16X-RAY DIFFRACTION16chain 'B' and (resid 138 through 151 )
17X-RAY DIFFRACTION17chain 'B' and (resid 152 through 169 )
18X-RAY DIFFRACTION18chain 'C' and (resid 2 through 14 )
19X-RAY DIFFRACTION19chain 'C' and (resid 15 through 41 )
20X-RAY DIFFRACTION20chain 'C' and (resid 42 through 64 )
21X-RAY DIFFRACTION21chain 'C' and (resid 65 through 74 )
22X-RAY DIFFRACTION22chain 'C' and (resid 75 through 84 )
23X-RAY DIFFRACTION23chain 'C' and (resid 85 through 122 )
24X-RAY DIFFRACTION24chain 'C' and (resid 123 through 135 )
25X-RAY DIFFRACTION25chain 'C' and (resid 136 through 145 )
26X-RAY DIFFRACTION26chain 'C' and (resid 146 through 164 )
27X-RAY DIFFRACTION27chain 'D' and (resid 2 through 14 )
28X-RAY DIFFRACTION28chain 'D' and (resid 15 through 41 )
29X-RAY DIFFRACTION29chain 'D' and (resid 42 through 64 )
30X-RAY DIFFRACTION30chain 'D' and (resid 65 through 74 )
31X-RAY DIFFRACTION31chain 'D' and (resid 75 through 84 )
32X-RAY DIFFRACTION32chain 'D' and (resid 85 through 122 )
33X-RAY DIFFRACTION33chain 'D' and (resid 123 through 135 )
34X-RAY DIFFRACTION34chain 'D' and (resid 136 through 145 )
35X-RAY DIFFRACTION35chain 'D' and (resid 146 through 164 )

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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