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- PDB-7jxq: EGFR kinase (T790M/V948R) in complex with allosteric inhibitor JB... -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 7jxq
タイトルEGFR kinase (T790M/V948R) in complex with allosteric inhibitor JBJ-09-063
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


response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity ...response to hydroxyisoflavone / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / positive regulation of protein kinase C activity / diterpenoid metabolic process / Shc-EGFR complex / ovulation cycle / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / response to UV-A / epidermal growth factor binding / PLCG1 events in ERBB2 signaling / tongue development / midgut development / ERBB2-EGFR signaling pathway / hydrogen peroxide metabolic process / PTK6 promotes HIF1A stabilization / digestive tract morphogenesis / morphogenesis of an epithelial fold / ERBB2 Activates PTK6 Signaling / intracellular vesicle / Signaling by EGFR / response to cobalamin / transmembrane receptor protein tyrosine kinase activator activity / protein tyrosine kinase activator activity / negative regulation of epidermal growth factor receptor signaling pathway / Signaling by ERBB4 / eyelid development in camera-type eye / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein insertion into membrane / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / Respiratory syncytial virus (RSV) attachment and entry / regulation of JNK cascade / : / PI3K events in ERBB2 signaling / positive regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of mitotic cell cycle / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / MAP kinase kinase kinase activity / embryonic placenta development / positive regulation of bone resorption / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / regulation of peptidyl-tyrosine phosphorylation / positive regulation of phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / cellular response to cadmium ion / EGFR Transactivation by Gastrin / positive regulation of DNA repair / GRB2 events in ERBB2 signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / positive regulation of synaptic transmission, glutamatergic / cellular response to dexamethasone stimulus / ossification / neurogenesis / regulation of ERK1 and ERK2 cascade / basal plasma membrane / neuron projection morphogenesis / positive regulation of superoxide anion generation / positive regulation of DNA replication / epithelial cell proliferation / Signal transduction by L1 / cellular response to estradiol stimulus / positive regulation of epithelial cell proliferation / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / liver regeneration / positive regulation of protein localization to plasma membrane / EGFR downregulation / cellular response to amino acid stimulus / positive regulation of smooth muscle cell proliferation / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / lung development / clathrin-coated endocytic vesicle membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / negative regulation of protein catabolic process / receptor protein-tyrosine kinase / Downregulation of ERBB2 signaling / kinase binding / ruffle membrane / positive regulation of miRNA transcription / cell-cell adhesion
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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-VNS / 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: 1.83 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 Cancer / 年: 2022
タイトル: An allosteric inhibitor against the therapy-resistant mutant forms of EGFR in non-small cell lung cancer.
著者: To, C. / Beyett, T.S. / Jang, J. / Feng, W.W. / Bahcall, M. / Haikala, H.M. / Shin, B.H. / Heppner, D.E. / Rana, J.K. / Leeper, B.A. / Soroko, K.M. / Poitras, M.J. / Gokhale, P.C. / ...著者: To, C. / Beyett, T.S. / Jang, J. / Feng, W.W. / Bahcall, M. / Haikala, H.M. / Shin, B.H. / Heppner, D.E. / Rana, J.K. / Leeper, B.A. / Soroko, K.M. / Poitras, M.J. / Gokhale, P.C. / Kobayashi, Y. / Wahid, K. / Kurppa, K.J. / Gero, T.W. / Cameron, M.D. / Ogino, A. / Mushajiang, M. / Xu, C. / Zhang, Y. / Scott, D.A. / Eck, M.J. / Gray, N.S. / Janne, P.A.
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4月27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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22022年5月11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
改定 1.32023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
B: Epidermal growth factor receptor
C: Epidermal growth factor receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)155,24716
ポリマ－150,8984
非ポリマー4,34912
水9,746541
1
B: Epidermal growth factor receptor
ヘテロ分子

D: Epidermal growth factor receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)77,6238
ポリマ－75,4492
非ポリマー2,1746
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area5070 Å2
ΔGint-44 kcal/mol
Surface area25930 Å2
手法PISA
2
A: 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)77,6238
ポリマ－75,4492
非ポリマー2,1746
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area5160 Å2
ΔGint-44 kcal/mol
Surface area25690 Å2
手法PISA
単位格子
Length a, b, c (Å)57.318, 74.598, 150.569
Angle α, β, γ (deg.)90.000, 98.690, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 701 through 765 or resid 767...
21(chain B and (resid 701 through 765 or resid 767...
31(chain C and (resid 701 through 765 or resid 767...
41(chain D and (resid 701 through 765 or resid 767...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 701 through 765 or resid 767...A701 - 765
121(chain A and (resid 701 through 765 or resid 767...A767 - 862
131(chain A and (resid 701 through 765 or resid 767...A700 - 1201
141(chain A and (resid 701 through 765 or resid 767...A890 - 907
151(chain A and (resid 701 through 765 or resid 767...A909 - 1093
211(chain B and (resid 701 through 765 or resid 767...B701 - 765
221(chain B and (resid 701 through 765 or resid 767...B767 - 862
231(chain B and (resid 701 through 765 or resid 767...B876 - 888
241(chain B and (resid 701 through 765 or resid 767...B890 - 907
251(chain B and (resid 701 through 765 or resid 767...B909 - 1094
311(chain C and (resid 701 through 765 or resid 767...C701 - 765
321(chain C and (resid 701 through 765 or resid 767...C767 - 862
331(chain C and (resid 701 through 765 or resid 767...C876 - 888
341(chain C and (resid 701 through 765 or resid 767...C890 - 907
351(chain C and (resid 701 through 765 or resid 767...C909 - 1091
411(chain D and (resid 701 through 765 or resid 767...D701 - 765
421(chain D and (resid 701 through 765 or resid 767...D767 - 862
431(chain D and (resid 701 through 765 or resid 767...D700 - 1201
441(chain D and (resid 701 through 765 or resid 767...D890 - 907
451(chain D and (resid 701 through 765 or resid 767...D909 - 1092

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要素

#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: 4 / 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
#2: 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
#3: 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
#4: 化合物
ChemComp-VNS / (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-{6-[4-(1-methylpiperidin-4-yl)phenyl]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}-N-(1,3-thiazol-2-yl)acetamide


分子量: 556.650 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C31H29FN4O3S / タイプ: SUBJECT OF INVESTIGATION
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 541 / 由来タイプ: 天然 / 式: H2O
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: 2.11 Å3/Da / 溶媒含有率: 41.67 % / 解説: Plate
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: 5.7 / 詳細: 0.1 M Bis-Tris pH 5.7, 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-E / 波長: 0.9792 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年11月10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: 0.9792 Å / 相対比: 1
反射解像度: 1.83→66.69 Å / Num. obs: 215143 / % possible obs: 99.5 % / 冗長度: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.038 / Rrim(I) all: 0.102 / Net I/σ(I): 9.3
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.83-1.887.11.7945802781160.5130.7171.9350.999.6
8.18-66.6970.028915713120.9990.0120.03131.899.9

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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
Aimless0.7.3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: 1.83→66.69 Å / SU ML: 0.23 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 25.2 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.218 3902 1.81 %
Rwork0.184 211241 -
obs0.1846 215143 98.92 %
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: 112.34 Å2 / Biso mean: 45.2554 Å2 / Biso min: 21.32 Å2
精密化ステップサイクル: final / 解像度: 1.83→66.69 Å
タンパク質核酸リガンド溶媒全体
原子数9569 0 288 541 10398
Biso mean--35.9 45.39 -
残基数----1189
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A5801X-RAY DIFFRACTION12.098TORSIONAL
12B5801X-RAY DIFFRACTION12.098TORSIONAL
13C5801X-RAY DIFFRACTION12.098TORSIONAL
14D5801X-RAY DIFFRACTION12.098TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.850.35331130.34747560767398
1.85-1.880.33371320.32847476760898
1.88-1.90.3231620.30617500766299
1.9-1.930.28581300.29237549767998
1.93-1.950.29751560.27937480763699
1.95-1.980.26381330.26637561769499
1.98-2.010.30181340.27057538767299
2.01-2.050.31911310.25177626775799
2.05-2.080.30591450.24137472761799
2.08-2.120.25941440.23017576772099
2.12-2.160.28021370.22287486762399
2.16-2.210.28481390.20627670780999
2.21-2.250.23071320.21287539767199
2.25-2.310.24241430.20127553769699
2.31-2.360.24111380.20687525766399
2.36-2.430.2741350.19737532766799
2.43-2.50.25781370.20797384752196
2.5-2.580.26561470.19927333748097
2.58-2.670.28781350.20327562769799
2.67-2.780.20861500.192775617711100
2.78-2.90.21411340.195176377771100
2.9-3.060.28371470.186876047751100
3.06-3.250.2241420.186176697811100
3.25-3.50.21421420.168776117753100
3.5-3.850.19341340.154376097743100
3.85-4.410.18211420.134276357777100
4.41-5.560.14361470.14637400754798
5.56-66.690.15711410.15537593773499
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)
16.2790.0282-1.17772.1642-1.28555.83120.0719-0.02330.0088-0.0379-0.1773-0.55070.04360.77810.18520.2625-0.0145-0.0370.3099-0.07540.28725.567-9.912-65.52
25.51970.5368-6.89664.51470.95082.04370.4913-0.27410.2988-0.0801-0.08130.0974-0.65980.4204-0.25850.29610.0129-0.04910.2808-0.04470.216116.38-4.771-60.392
33.77780.53420.85633.73020.64292.06470.2869-0.46630.26470.20650.0282-0.438-0.46820.7252-0.18840.2652-0.0267-0.03970.3269-0.04730.298723.308-6.591-65.271
42.45030.5704-1.572.1674-0.53033.4794-0.0367-0.21810.04090.24040.0709-0.04420.04660.1834-0.01770.2730.0411-0.00720.18880.0050.227310.4-17.315-55.246
52.9868-0.02560.65612.69860.92215.8184-0.0495-0.2923-0.17430.33770.1550.37040.5547-0.5501-0.09220.3217-0.00460.09110.26770.08950.3157-4.903-21.622-46.901
66.67422.4409-6.57761.1239-1.68397.45530.14190.3309-0.0057-0.02120.24150.7680.2781-0.9452-0.29720.3926-0.0206-0.00690.45030.1070.5268-4.766-18.57-71.703
74.4812-1.1236-2.25553.88270.40796.79240.45850.24820.60640.1676-0.21520.9009-0.3986-1.0108-0.29240.23130.09510.05730.44840.1530.481313.38-26.753-8.061
83.3607-0.5462-2.21693.0593-0.12737.36140.45450.51750.8199-0.37480.089-0.0629-0.8397-0.3321-0.48270.35780.07390.12510.28650.14790.517621.932-21.518-14.153
93.1725-0.46210.17892.44830.84918.70010.24280.36580.5565-0.05060.16740.1152-0.9422-1.1614-0.26970.27820.10810.10940.39110.15860.51315.547-23.414-8.696
109.2902-4.14632.11524.2219-0.47325.46280.27630.6797-0.1692-0.3162-0.08330.41130.3415-0.8587-0.25410.2536-0.07320.00210.42260.07990.297416.734-36.85-16.796
114.7911-0.3793-1.89213.2240.8524.99020.24370.01030.97-0.25810.2847-0.3-0.52010.1364-0.43160.3121-0.03050.09080.18510.03070.365630.342-25.637-13.982
123.05490.529-1.89573.40161.11335.9290.07560.44450.2734-0.36370.19090.06270.0819-0.3249-0.22770.1986-0.0094-0.00140.23290.06570.258831.179-36.327-23.036
135.34440.3729-0.02973.32181.22286.95160.08780.1970.1726-0.27640.3245-0.66930.07490.9749-0.40670.28060.00160.11850.3522-0.09090.414744.009-36.914-27.115
148.1552-1.4228-0.20087.35291.26212.04730.24740.4153-0.493-0.8323-0.1157-0.2660.60710.4103-0.16770.43980.04770.02990.4879-0.1070.325536.921-36.020.19
155.5897-1.3072-1.82036.48061.05197.18730.1329-0.11050.25930.08040.255-0.8439-0.40840.5891-0.33780.2655-0.0536-0.08180.2417-0.1010.31919.662-44.921-60.777
163.39660.50620.82064.3654-1.49289.43570.1741-0.1591-0.06480.31240.1807-0.7375-0.99611.1406-0.1780.287-0.1034-0.06680.3373-0.10730.463321.478-44.143-62.739
176.60846.43526.85016.30996.68267.24290.2067-0.247-0.75771.03560.3617-1.13430.38870.7063-0.68880.51680.1335-0.17090.5048-0.07660.57225.845-56.585-51.723
183.17850.2367-1.27453.1864-0.53082.9644-0.1226-0.41830.15940.49210.2442-0.1329-0.0730.0212-0.09110.290.0654-0.03640.24-0.04340.18035.818-57.285-53.392
193.7128-0.6211-0.47563.46370.01796.5108-0.151-0.6473-0.21210.63350.36220.34410.2669-0.5251-0.23880.39340.05390.05890.43170.1370.291-6.955-63.628-46.299
208.13384.1153-7.3732.1031-3.09232.4044-0.10770.3697-0.07540.02420.25350.35030.2176-0.9037-0.23940.4354-0.0651-0.03530.73810.0510.3214-5.588-57.322-70.395
212.7536-0.3328-0.54636.45740.69145.59010.12110.01070.24510.0017-0.0030.6198-0.3313-0.8156-0.08090.25870.1111-0.01330.42390.13520.387918.976-61.567-12.079
222.9599-0.1164-0.18864.60671.58079.13860.0520.42490.5145-0.20470.02630.414-0.8302-1.51230.05660.35380.14550.06290.51440.18780.47817.744-60.041-10.07
239.5142-6.73732.00555.2802-6.84982.02750.53030.2699-0.3488-0.72490.30710.79870.3423-1.2069-0.65540.4388-0.0393-0.08580.77150.11470.448912.073-72.749-20.59
242.2741-0.9078-0.53182.54940.75063.03120.08210.10450.2464-0.21080.0499-0.0374-0.0582-0.1545-0.1370.22310.00360.00920.23780.09230.200332.519-72.608-15.786
252.6670.1802-0.76781.8515-0.2294.30670.12250.64750.4821-0.4517-0.01670.0742-0.179-0.4205-0.13020.32360.0530.03030.37120.12170.2633.788-73.383-32.482
263.82720.11-0.12932.30510.08725.31140.07570.2127-0.105-0.2193-0.0152-0.29910.4320.3964-0.03770.32840.06240.0520.2690.00960.311145.035-83.431-26.914
274.2166-3.0085-5.18612.00212.88622.4556-0.0647-0.30060.1487-0.12260.284-0.45040.10360.751-0.21680.3531-0.0091-0.02260.5554-0.00690.38445.165-73.841-5.066
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND RESID 700:717 )D700 - 717
2X-RAY DIFFRACTION2( CHAIN D AND RESID 718:731 )D718 - 731
3X-RAY DIFFRACTION3( CHAIN D AND RESID 732:752 )D732 - 752
4X-RAY DIFFRACTION4( CHAIN D AND RESID 753:892 )D753 - 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 700:717 )A700 - 717
8X-RAY DIFFRACTION8( CHAIN A AND RESID 718:731 )A718 - 731
9X-RAY DIFFRACTION9( CHAIN A AND RESID 732:752 )A732 - 752
10X-RAY DIFFRACTION10( CHAIN A AND RESID 753:778 )A753 - 778
11X-RAY DIFFRACTION11( CHAIN A AND RESID 779:810 )A779 - 810
12X-RAY DIFFRACTION12( CHAIN A AND RESID 811:892 )A811 - 892
13X-RAY DIFFRACTION13( CHAIN A AND RESID 893:991 )A893 - 991
14X-RAY DIFFRACTION14( CHAIN A AND RESID 992:1007 )A992 - 1007
15X-RAY DIFFRACTION15( CHAIN B AND RESID 701:731 )B701 - 731
16X-RAY DIFFRACTION16( CHAIN B AND RESID 732:752 )B732 - 752
17X-RAY DIFFRACTION17( CHAIN B AND RESID 753:768 )B753 - 768
18X-RAY DIFFRACTION18( CHAIN B AND RESID 769:908 )B769 - 908
19X-RAY DIFFRACTION19( CHAIN B AND RESID 909:978 )B909 - 978
20X-RAY DIFFRACTION20( CHAIN B AND RESID 979:1007 )B979 - 1007
21X-RAY DIFFRACTION21( CHAIN C AND RESID 700:731 )C700 - 731
22X-RAY DIFFRACTION22( CHAIN C AND RESID 732:752 )C732 - 752
23X-RAY DIFFRACTION23( CHAIN C AND RESID 753:768 )C753 - 768
24X-RAY DIFFRACTION24( CHAIN C AND RESID 769:853 )C769 - 853
25X-RAY DIFFRACTION25( CHAIN C AND RESID 854:928 )C854 - 928
26X-RAY DIFFRACTION26( CHAIN C AND RESID 929:978 )C929 - 978
27X-RAY DIFFRACTION27( CHAIN C AND RESID 979:1007 )C979 - 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://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