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- PDB-7jxp: EGFR kinase (T790M/V948R) in complex with osimertinib and JBJ-04-... -

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基本情報

登録情報
データベース: PDB / ID: 7jxp
タイトルEGFR kinase (T790M/V948R) in complex with osimertinib and JBJ-04-125-02
要素Epidermal growth factor receptor
キーワードTRANSFERASE/TRANSFERASE Inhibitor / EGFR / ErbB1 / kinase / inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
機能・相同性
機能・相同性情報


multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / epidermal growth factor receptor activity / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A ...multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / epidermal growth factor receptor activity / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / Signaling by EGFR / intracellular vesicle / eyelid development in camera-type eye / negative regulation of epidermal growth factor receptor signaling pathway / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / protein tyrosine kinase activator activity / Respiratory syncytial virus (RSV) attachment and entry / Signaling by ERBB4 / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hair follicle development / MAP kinase kinase kinase activity / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / salivary gland morphogenesis / Signaling by ERBB2 / GRB2 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / SHC1 events in EGFR signaling / transmembrane receptor protein tyrosine kinase activity / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / SHC1 events in ERBB2 signaling / ossification / NOTCH3 Activation and Transmission of Signal to the Nucleus / positive regulation of DNA repair / basal plasma membrane / cellular response to epidermal growth factor stimulus / EGFR downregulation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / positive regulation of epithelial cell proliferation / positive regulation of protein localization to plasma membrane / cellular response to amino acid stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Downregulation of ERBB2 signaling / cell-cell adhesion / receptor protein-tyrosine kinase / negative regulation of protein catabolic process / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of miRNA transcription / kinase binding / ruffle membrane / positive regulation of protein phosphorylation / epidermal growth factor receptor signaling pathway / neuron differentiation / cell morphogenesis / positive regulation of fibroblast proliferation / HCMV Early Events / Constitutive Signaling by Aberrant PI3K in Cancer / actin filament binding / Cargo recognition for clathrin-mediated endocytosis / cell junction / transmembrane signaling receptor activity / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / positive regulation of canonical Wnt signaling pathway / Clathrin-mediated endocytosis / PIP3 activates AKT signaling / virus receptor activity / ATPase binding / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / double-stranded DNA binding / protein tyrosine kinase activity / early endosome membrane / protein phosphatase binding / nuclear membrane / basolateral plasma membrane / learning or memory / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / endosome membrane
類似検索 - 分子機能
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-JBJ / Chem-YY3 / Epidermal growth factor receptor
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: 2.16 Å
データ登録者Beyett, T.S. / Eck, M.J.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA201049-05 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)1F32CA247198-01 米国
引用ジャーナル: Nat Commun / 年: 2022
タイトル: Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors
著者: Beyett, T.S. / To, C. / Heppner, D.E. / Rana, J.K. / Schmoker, A.M. / Jang, J. / De Clercq, D.J.H. / Gomez, G. / Scott, D.A. / Gray, N.S. / Janne, P.A. / Eck, M.J.
履歴
登録2020年8月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年9月8日Provider: repository / タイプ: Initial release
改定 1.12022年5月18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_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
改定 1.22023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.32024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
D: Epidermal growth factor receptor
A: Epidermal growth factor receptor
C: Epidermal growth factor receptor
F: Epidermal growth factor receptor
B: Epidermal growth factor receptor
E: Epidermal growth factor receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)232,73022
ポリマ－226,3486
非ポリマー6,38316
水5,386299
1
D: Epidermal growth factor receptor
ヘテロ分子

F: Epidermal growth factor receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,5978
ポリマ－75,4492
非ポリマー2,1486
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area5290 Å2
ΔGint-45 kcal/mol
Surface area26340 Å2
手法PISA
2
A: Epidermal growth factor receptor
E: Epidermal growth factor receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,5677
ポリマ－75,4492
非ポリマー2,1175
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-32 kcal/mol
Surface area26270 Å2
手法PISA
3
B: Epidermal growth factor receptor
ヘテロ分子

C: Epidermal growth factor receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,5677
ポリマ－75,4492
非ポリマー2,1175
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4220 Å2
ΔGint-31 kcal/mol
Surface area26610 Å2
手法PISA
単位格子
Length a, b, c (Å)57.113, 94.741, 95.569
Angle α, β, γ (deg.)70.560, 78.400, 79.180
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 700 through 765 or resid 767...
21(chain B and (resid 700 through 765 or resid 767...
31(chain C and (resid 700 through 765 or resid 767 through 907 or resid 909 through 1007))
41(chain D and (resid 700 through 765 or resid 767...
51(chain E and (resid 700 through 765 or resid 767 through 907 or resid 909 through 1007))
61(chain F and (resid 700 through 765 or resid 767...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNVALVAL(chain A and (resid 700 through 765 or resid 767...AB700 - 7659 - 74
12ALAALAALAALA(chain A and (resid 700 through 765 or resid 767...AB767 - 85976 - 168
13VALVALLEULEU(chain A and (resid 700 through 765 or resid 767...AB876 - 907185 - 216
14THRTHRMETMET(chain A and (resid 700 through 765 or resid 767...AB909 - 1007218 - 316
21ASNASNVALVAL(chain B and (resid 700 through 765 or resid 767...BE700 - 7659 - 74
22ALAALAALAALA(chain B and (resid 700 through 765 or resid 767...BE767 - 85976 - 168
23VALVALLEULEU(chain B and (resid 700 through 765 or resid 767...BE876 - 907185 - 216
24THRTHRMETMET(chain B and (resid 700 through 765 or resid 767...BE909 - 1007218 - 316
31ASNASNVALVAL(chain C and (resid 700 through 765 or resid 767 through 907 or resid 909 through 1007))CC700 - 7659 - 74
32ALAALALEULEU(chain C and (resid 700 through 765 or resid 767 through 907 or resid 909 through 1007))CC767 - 90776 - 216
33THRTHRMETMET(chain C and (resid 700 through 765 or resid 767 through 907 or resid 909 through 1007))CC909 - 1007218 - 316
41ASNASNVALVAL(chain D and (resid 700 through 765 or resid 767...DA700 - 7659 - 74
42ALAALAALAALA(chain D and (resid 700 through 765 or resid 767...DA767 - 85976 - 168
43VALVALLEULEU(chain D and (resid 700 through 765 or resid 767...DA876 - 907185 - 216
44THRTHRMETMET(chain D and (resid 700 through 765 or resid 767...DA909 - 1007218 - 316
51ASNASNVALVAL(chain E and (resid 700 through 765 or resid 767 through 907 or resid 909 through 1007))EF700 - 7659 - 74
52ALAALALEULEU(chain E and (resid 700 through 765 or resid 767 through 907 or resid 909 through 1007))EF767 - 90776 - 216
53THRTHRMETMET(chain E and (resid 700 through 765 or resid 767 through 907 or resid 909 through 1007))EF909 - 1007218 - 316
61ASNASNVALVAL(chain F and (resid 700 through 765 or resid 767...FD700 - 7659 - 74
62ALAALAALAALA(chain F and (resid 700 through 765 or resid 767...FD767 - 85976 - 168
63VALVALLEULEU(chain F and (resid 700 through 765 or resid 767...FD876 - 907185 - 216
64THRTHRMETMET(chain F and (resid 700 through 765 or resid 767...FD909 - 1007218 - 316

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要素

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タンパク質 , 1種, 6分子 DACFBE

#1: タンパク質
Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


分子量: 37724.598 Da / 分子数: 6 / 断片: kinase domain / 変異: T790M, V948R / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EGFR, ERBB, ERBB1, HER1 / プラスミド: pTriEX / 細胞株 (発現宿主): Sf9
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P00533, receptor protein-tyrosine kinase

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非ポリマー , 5種, 315分子

#2: 化合物
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP


分子量: 506.196 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C10H17N6O12P3
コメント: AMP-PNP, エネルギー貯蔵分子類似体*YM
#3: 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: 4 / 由来タイプ: 合成 / 式: Mg
#4: 化合物
ChemComp-JBJ / (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-{1-oxo-6-[4-(piperazin-1-yl)phenyl]-1,3-dihydro-2H-isoindol-2-yl}-N-(1,3-thiazol-2-yl)acetamide


分子量: 543.612 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C29H26FN5O3S / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物 ChemComp-YY3 / N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-{[4-(1-methyl-1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)prop-2-enamide / Osimertinib / AZD 9291 / オシメルチニブ


分子量: 499.607 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C28H33N7O2 / タイプ: SUBJECT OF INVESTIGATION / コメント: 薬剤, 阻害剤*YM
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 299 / 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
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: 2.09 Å3/Da / 溶媒含有率: 41.21 % / Mosaicity: 0.148 °
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5 / 詳細: 0.1 M Bis-Tris pH 5.5, 28% (w/v) 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-C / 波長: 0.9793 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年7月15日
放射モノクロメーター: Double Crystal / 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: 0.9793 Å / 相対比: 1
反射解像度: 2.16→89.11 Å / Num. obs: 81966 / % possible obs: 83.3 % / 冗長度: 3.6 % / Biso Wilson estimate: 35.135 Å2 / Rpim(I) all: 0.066 / Rrim(I) all: 0.128 / Net I/σ(I): 6.2 / Num. measured all: 295266
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.16-2.23.11.1678521630.771.42843.4
5.86-89.183.813.11672644370.0350.06890.3

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2_3874精密化
xia2データスケーリング
PDB_EXTRACT3.25データ抽出
xia2データ削減
PHASER位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 5D41

5d41


解像度: 2.16→89.11 Å / SU ML: 0.29 / 交差検証法: THROUGHOUT / σ(F): 1.96 / 位相誤差: 31.27 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2473 4040 4.94 %
Rwork0.2122 77710 -
obs0.2139 81750 83.12 %
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 max: 152.15 Å2 / Biso mean: 57.9814 Å2 / Biso min: 23.47 Å2
精密化ステップサイクル: final / 解像度: 2.16→89.11 Å
タンパク質核酸リガンド溶媒全体
原子数14364 0 436 299 15099
Biso mean--50.29 50.13 -
残基数----1783
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A8750X-RAY DIFFRACTION6.255TORSIONAL
12B8750X-RAY DIFFRACTION6.255TORSIONAL
13C8750X-RAY DIFFRACTION6.255TORSIONAL
14D8750X-RAY DIFFRACTION6.255TORSIONAL
15E8750X-RAY DIFFRACTION6.255TORSIONAL
16F8750X-RAY DIFFRACTION6.255TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.16-2.190.399600.3181331139141
2.19-2.210.3284870.30971548163548
2.21-2.240.2718820.30531609169150
2.24-2.270.3775930.32271788188155
2.27-2.30.28661050.31041988209361
2.3-2.330.29751030.30062116221967
2.33-2.370.34391240.28712363248773
2.37-2.410.34681220.29122692281483
2.41-2.450.29261630.27443021318495
2.45-2.490.31241740.26943036321094
2.49-2.530.34421550.26483009316494
2.53-2.580.30871550.26163014316993
2.58-2.630.31611750.26362959313493
2.63-2.690.30921690.24572923309292
2.69-2.750.27261720.24352889306191
2.75-2.820.28151530.23032790294386
2.82-2.90.28341660.22323026319294
2.9-2.980.27191490.22143085323495
2.98-3.080.26121280.22773010313894
3.08-3.190.28231570.22823049320693
3.19-3.320.28151270.22812928305591
3.32-3.470.28091460.20852740288685
3.47-3.650.21831740.20373034320895
3.65-3.880.1951740.18223049322395
3.88-4.180.2151440.18092982312693
4.18-4.60.18021530.16422810296387
4.6-5.270.20341270.18023099322695
5.27-6.640.22981490.20042887303690
6.64-89.110.20991540.17452935308991
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)
15.0199-0.05640.3594.47510.26565.552-0.13290.21690.385-0.4493-0.38091.1398-0.1922-0.83250.470.37470.0235-0.15820.3911-0.10750.5778-35.85821.184-47.291
25.99090.43612.02292.2216-1.08913.30870.47130.4035-1.0773-0.1526-0.43390.66860.6668-0.5844-0.09070.3617-0.07770.05930.4213-0.23390.6984-36.0518.923-40.102
34.0636-0.73421.33084.05440.51033.2514-0.23630.27560.5343-0.5882-0.1442-0.051-0.2168-0.09310.3360.4282-0.0305-0.05080.21420.00790.2572-21.90317.264-47.473
42.8092-1.0391-0.55834.85171.56373.8519-0.01550.0591-0.1360.0437-0.2050.32190.389-0.45550.25450.2655-0.04350.02870.21570.04370.2038-21.2163.806-42.769
54.79731.45360.49735.54391.71613.7498-0.02860.0199-0.8231-0.02170.0863-0.85650.47580.3172-0.04380.30770.03630.05460.21540.05050.4836-9.939-2.134-45.064
62.4441-3.4546-1.97555.86324.02142.97930.1356-0.92390.88630.1280.4007-0.849-0.03180.8261-0.60490.3731-0.0867-0.00240.5099-0.01990.6431-8.33420.354-34.632
73.0448-0.6314-1.2642.78860.52813.49130.08950.27990.269-0.11110.0384-0.4715-0.21540.1039-0.13870.2586-0.0093-0.00180.22690.03180.2887-38.847-33.036-56.001
82.6853-1.57240.68234.4914-3.92873.6218-0.3452-0.57881.36541.1020.4276-1.2747-1.21240.5238-0.29810.61240.0742-0.00330.4766-0.13350.7999-35.397-18.647-45.837
94.6356-0.38940.11855.04461.06512.7230.0588-0.28450.49890.62480.10870.0227-0.3833-0.2732-0.15170.42920.09670.07210.32610.03150.2321-54.647-23.982-40.892
104.2851-2.9768-3.07495.0163.42052.60890.21751.1424-0.9223-0.09-0.68041.12650.2247-1.15590.45860.4183-0.0194-0.00950.8864-0.11170.5568-59.037-42.271-59.152
112.86690.0091-0.84794.87340.12143.3084-0.00710.04580.981-0.52140.5189-0.9913-0.62480.4206-0.54480.525-0.14580.22540.5380.02741.0174-33.63-9.591-93.158
122.2871.1370.38763.7890.33664.1312-0.1041-0.03110.7746-0.1430.4815-1.3472-0.62070.7965-0.29040.4079-0.05250.02240.489-0.12031.0335-31.575-10.479-86.857
132.85010.6131-1.69675.65040.80695.8306-0.04220.48310.2172-0.538-0.1040.151-0.3592-0.65250.13640.3829-0.003-0.08410.2468-0.03440.2949-52.498-9.973-89.076
142.1616-0.88820.23214.32761.5943.7427-0.1088-0.52350.65920.40740.0864-0.6274-0.24170.17180.02340.2907-0.0009-0.08670.3433-0.10090.4206-48.722-8.651-74.462
153.2187-0.52080.33544.44011.49113.5696-0.242-0.91870.70460.688-0.10270.2032-0.1253-0.61570.33230.41120.0608-0.03680.7005-0.24470.4691-59.199-5.739-68.751
162.6323-2.5442-3.32164.40644.33994.5958-0.11210.1283-0.55840.208-0.69361.43790.4329-0.72560.71560.365-0.10580.01930.6972-0.23740.7831-59.72-22.917-87.295
175.7103-0.3045-1.16245.99031.02555.1517-0.0507-0.1510.3963-0.25960.038-0.5229-0.46190.2915-0.08740.3356-0.054-0.00910.2670.01080.4426-32.11-53.273-35.061
184.64920.3416-0.64686.33391.7695.0089-0.1599-0.12350.5873-0.67310.3762-0.7317-0.69270.8312-0.20090.3576-0.04860.01160.33750.03190.5118-30.878-53.756-36.988
197.73323.1583-2.25845.3744-1.0515.40760.1311-0.44380.92690.6877-0.2647-0.0156-0.40770.41670.1910.32820.0471-0.09760.3018-0.04580.5278-30.945-55.135-21.604
207.007-0.8454-0.84282.29420.16454.94090.3040.35440.5747-0.2415-0.49190.5201-0.444-0.69560.17170.40650.0692-0.14550.2891-0.11570.5758-45.455-52.077-31.797
211.8383-2.4954-0.22463.2599-0.09364.2843-0.2715-0.26640.67770.409-0.1935-0.0106-0.4243-0.17790.48010.33810.004-0.10530.3702-0.1730.5939-45.843-50.975-17.634
222.556-0.22870.93922.9256-0.22743.7857-0.2354-0.5240.56930.3906-0.19450.6329-0.5324-1.03450.42650.47840.11980.01220.6752-0.28530.7755-57.001-46.83-12.674
233.7745-2.5084-2.15041.66511.51551.15120.0561-0.0521-0.6299-0.0267-0.5441.49520.3217-0.84890.57320.407-0.04570.00330.866-0.39291.1441-58.695-65.381-29.068
243.2678-1.76310.76567.17010.56443.18630.0860.3788-0.1417-0.682-0.39180.4656-0.1686-0.64610.18260.37990.07840.02450.5095-0.03080.2955-35.6580.425-17.071
252.7316-1.80250.36925.9680.32912.71960.06990.32340.1182-0.2396-0.0859-0.22040.0242-0.20010.03150.26690.0010.10020.3438-0.01440.2191-26.163-7.365-13.608
262.77662.02712.20871.4591.60591.6092-0.06890.4348-0.2703-1.1438-0.25920.42810.5099-0.34610.18790.72810.0360.08430.454-0.04340.6258-32.297-19.738-24.685
272.3184-1.43723.04182.83940.79587.76140.13630.5573-0.5042-0.498-0.10510.27090.6483-0.72940.13410.4581-0.05310.09970.4015-0.17610.3923-24.143-25.009-24.666
282.7810.0113-0.2185.47661.97626.0864-0.10580.2004-0.3635-0.12170.3256-1.14770.54850.8243-0.21260.36170.08180.1210.3758-0.05050.6537-10.104-22.09-17.8
293.1087-2.2633-1.27382.31121.77771.4308-0.0219-0.35520.2686-0.09440.4391-1.62380.19190.9086-0.40740.4335-0.00290.08610.6548-0.18651.1167-8.135-0.318-5.711
306.350.6433-1.34676.36560.82543.7996-0.33261.1488-0.4688-1.26190.04090.6532-0.397-0.52240.16660.5751-0.0422-0.17941.0366-0.01040.4663-52.53-49-77.669
312.20321.0786-0.8696.03930.76172.5712-0.48941.0828-0.9105-0.75340.4684-0.70540.2433-0.39750.030.5448-0.2160.18040.8182-0.37180.659-42.88-61.424-74.097
321.0330.298-1.232.11150.17542.1903-0.85730.1792-1.8528-0.4886-0.1958-1.63670.80310.33590.7460.9789-0.0510.49350.676-0.66481.9081-27.838-74.633-73.649
331.8593-1.6253-0.90911.72941.03690.9055-0.2206-0.1694-0.5339-0.04480.5232-2.11590.3520.8911-0.32360.559-0.05310.03880.8144-0.29861.4416-26.928-52.081-62.311
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND RESID 700:752 )D700 - 752
2X-RAY DIFFRACTION2( CHAIN D AND RESID 753:778 )D753 - 778
3X-RAY DIFFRACTION3( CHAIN D AND RESID 779:810 )D779 - 810
4X-RAY DIFFRACTION4( CHAIN D AND RESID 811:892 )D811 - 892
5X-RAY DIFFRACTION5( CHAIN D AND RESID 893:978 )D893 - 978
6X-RAY DIFFRACTION6( CHAIN D AND RESID 979:1007 )D979 - 1007
7X-RAY DIFFRACTION7( CHAIN A AND RESID 700:853 )A700 - 853
8X-RAY DIFFRACTION8( CHAIN A AND RESID 854:877 )A854 - 877
9X-RAY DIFFRACTION9( CHAIN A AND RESID 878:978 )A878 - 978
10X-RAY DIFFRACTION10( CHAIN A AND RESID 979:1007 )A979 - 1007
11X-RAY DIFFRACTION11( CHAIN C AND RESID 700:731 )C700 - 731
12X-RAY DIFFRACTION12( CHAIN C AND RESID 732:786 )C732 - 786
13X-RAY DIFFRACTION13( CHAIN C AND RESID 787:810 )C787 - 810
14X-RAY DIFFRACTION14( CHAIN C AND RESID 811:908 )C811 - 908
15X-RAY DIFFRACTION15( CHAIN C AND RESID 909:978 )C909 - 978
16X-RAY DIFFRACTION16( CHAIN C AND RESID 979:1007 )C979 - 1007
17X-RAY DIFFRACTION17( CHAIN F AND RESID 700:731 )F700 - 731
18X-RAY DIFFRACTION18( CHAIN F AND RESID 732:752 )F732 - 752
19X-RAY DIFFRACTION19( CHAIN F AND RESID 753:778 )F753 - 778
20X-RAY DIFFRACTION20( CHAIN F AND RESID 779:810 )F779 - 810
21X-RAY DIFFRACTION21( CHAIN F AND RESID 811:892 )F811 - 892
22X-RAY DIFFRACTION22( CHAIN F AND RESID 893:978 )F893 - 978
23X-RAY DIFFRACTION23( CHAIN F AND RESID 979:1007 )F979 - 1007
24X-RAY DIFFRACTION24( CHAIN B AND RESID 700:731 )B700 - 731
25X-RAY DIFFRACTION25( CHAIN B AND RESID 732:853 )B732 - 853
26X-RAY DIFFRACTION26( CHAIN B AND RESID 854:873 )B854 - 873
27X-RAY DIFFRACTION27( CHAIN B AND RESID 874:892 )B874 - 892
28X-RAY DIFFRACTION28( CHAIN B AND RESID 893:978 )B893 - 978
29X-RAY DIFFRACTION29( CHAIN B AND RESID 979:1007 )B979 - 1007
30X-RAY DIFFRACTION30( CHAIN E AND RESID 700:731 )E700 - 731
31X-RAY DIFFRACTION31( CHAIN E AND RESID 732:908 )E732 - 908
32X-RAY DIFFRACTION32( CHAIN E AND RESID 909:978 )E909 - 978
33X-RAY DIFFRACTION33( CHAIN E AND RESID 979:1007 )E979 - 1007

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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