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- PDB-9axx: Crystal structure of BRAF/MEK1 complex with NST-628 and an active... -

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基本情報

登録情報
データベース: PDB / ID: 9axx
タイトルCrystal structure of BRAF/MEK1 complex with NST-628 and an active RAF dimer
要素
  • Dual specificity mitogen-activated protein kinase kinase 1
  • Serine/threonine-protein kinase B-raf
キーワードTRANSFERASE / Inhibitor / complex / SIGNALING PROTEIN
機能・相同性
機能・相同性情報


epithelial cell proliferation involved in lung morphogenesis / negative regulation of homotypic cell-cell adhesion / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / positive regulation of endodermal cell differentiation / regulation of vascular associated smooth muscle contraction / CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / mitogen-activated protein kinase kinase / Golgi inheritance / placenta blood vessel development ...epithelial cell proliferation involved in lung morphogenesis / negative regulation of homotypic cell-cell adhesion / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / positive regulation of endodermal cell differentiation / regulation of vascular associated smooth muscle contraction / CD4-positive, alpha-beta T cell differentiation / positive regulation of axon regeneration / mitogen-activated protein kinase kinase / Golgi inheritance / placenta blood vessel development / MAP-kinase scaffold activity / positive regulation of muscle contraction / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / labyrinthine layer development / cerebellar cortex formation / regulation of axon regeneration / melanosome transport / type B pancreatic cell proliferation / Signalling to p38 via RIT and RIN / head morphogenesis / central nervous system neuron differentiation / ARMS-mediated activation / myeloid progenitor cell differentiation / endothelial cell apoptotic process / Signaling by MAP2K mutants / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of D-glucose transmembrane transport / vesicle transport along microtubule / negative regulation of fibroblast migration / establishment of protein localization to membrane / positive regulation of axonogenesis / positive regulation of Ras protein signal transduction / regulation of Golgi inheritance / mitogen-activated protein kinase kinase kinase binding / triglyceride homeostasis / regulation of T cell differentiation / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / mitogen-activated protein kinase kinase binding / regulation of stress-activated MAPK cascade / Frs2-mediated activation / stress fiber assembly / MAPK3 (ERK1) activation / ERBB2-ERBB3 signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / endodermal cell differentiation / face development / positive regulation of ATP biosynthetic process / MAP kinase kinase activity / Bergmann glial cell differentiation / synaptic vesicle exocytosis / Uptake and function of anthrax toxins / thyroid gland development / protein kinase activator activity / somatic stem cell population maintenance / positive regulation of peptidyl-serine phosphorylation / MAP kinase kinase kinase activity / positive regulation of protein serine/threonine kinase activity / postsynaptic modulation of chemical synaptic transmission / response to glucocorticoid / response to axon injury / negative regulation of endothelial cell apoptotic process / Schwann cell development / response to cAMP / keratinocyte differentiation / positive regulation of stress fiber assembly / ERK1 and ERK2 cascade / myelination / positive regulation of autophagy / positive regulation of substrate adhesion-dependent cell spreading / protein serine/threonine/tyrosine kinase activity / substrate adhesion-dependent cell spreading / dendrite cytoplasm / cellular response to calcium ion / insulin-like growth factor receptor signaling pathway / MAP3K8 (TPL2)-dependent MAPK1/3 activation / thymus development / protein serine/threonine kinase activator activity / animal organ morphogenesis / neuron projection morphogenesis / Signal transduction by L1 / cell motility / positive regulation of transcription elongation by RNA polymerase II / RAF activation / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / cellular response to nerve growth factor stimulus / ribosomal protein S6 kinase activity / Spry regulation of FGF signaling / histone H2AT120 kinase activity / histone H2BS36 kinase activity
類似検索 - 分子機能
: / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. ...: / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, 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 / Serine/threonine-protein kinase B-raf / Dual specificity mitogen-activated protein kinase kinase 1
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: 2.07 Å
データ登録者Quade, B. / Huang, X.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Cancer Discov / 年: 2024
タイトル: The Pan-RAF-MEK Nondegrading Molecular Glue NST-628 Is a Potent and Brain-Penetrant Inhibitor of the RAS-MAPK Pathway with Activity across Diverse RAS- and RAF-Driven Cancers.
著者: Meagan B Ryan / Bradley Quade / Natasha Schenk / Zhong Fang / Marshall Zingg / Steven E Cohen / Brooke M Swalm / Chun Li / Ayşegül Özen / Chaoyang Ye / Maria Stella Ritorto / Xin Huang / ...著者: Meagan B Ryan / Bradley Quade / Natasha Schenk / Zhong Fang / Marshall Zingg / Steven E Cohen / Brooke M Swalm / Chun Li / Ayşegül Özen / Chaoyang Ye / Maria Stella Ritorto / Xin Huang / Arvin C Dar / Yongxin Han / Klaus P Hoeflich / Michael Hale / Margit Hagel /
要旨: Alterations in the RAS-MAPK signaling cascade are common across multiple solid tumor types and are a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents the ...Alterations in the RAS-MAPK signaling cascade are common across multiple solid tumor types and are a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents the phosphorylation and activation of MEK by RAF, overcoming the limitations of traditional RAS-MAPK inhibitors and leading to deep durable inhibition of the pathway. Cellular, biochemical, and structural analyses of RAF-MEK complexes show that NST-628 engages all isoforms of RAF and prevents the formation of BRAF-CRAF heterodimers, a differentiated mechanism from all current RAF inhibitors. With a potent and durable inhibition of the RAF-MEK signaling complex as well as high intrinsic permeability into the brain, NST-628 demonstrates broad efficacy in cellular and patient-derived tumor models harboring diverse MAPK pathway alterations, including orthotopic intracranial models. Given its functional and pharmacokinetic mechanisms that are differentiated from previous therapies, NST-628 is positioned to make an impact clinically in areas of unmet patient need. Significance: This study introduces NST-628, a molecular glue having differentiated mechanism and drug-like properties. NST-628 treatment leads to broad efficacy with high tolerability and central nervous system activity across multiple RAS- and RAF-driven tumor models. NST-628 has the potential to provide transformative clinical benefits as both monotherapy and vertical combination anchor.
履歴
登録2024年3月6日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年4月17日Provider: repository / タイプ: Initial release
改定 1.12024年7月10日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

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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: Dual specificity mitogen-activated protein kinase kinase 1
B: Serine/threonine-protein kinase B-raf
C: Dual specificity mitogen-activated protein kinase kinase 1
D: Serine/threonine-protein kinase B-raf
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,09023
ポリマ－132,7414
非ポリマー3,34919
水5,657314
1
B: Serine/threonine-protein kinase B-raf
C: Dual specificity mitogen-activated protein kinase kinase 1
ヘテロ分子

A: Dual specificity mitogen-activated protein kinase kinase 1
D: Serine/threonine-protein kinase B-raf
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)136,09023
ポリマ－132,7414
非ポリマー3,34919
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
単位格子
Length a, b, c (Å)72.213, 82.408, 121.552
Angle α, β, γ (deg.)90.000, 105.650, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

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タンパク質 , 2種, 4分子 ACBD

#1: タンパク質 Dual specificity mitogen-activated protein kinase kinase 1 / MAP kinase kinase 1 / MAPKK 1 / MKK1 / ERK activator kinase 1 / MAPK/ERK kinase 1 / MEK 1


分子量: 34543.836 Da / 分子数: 2 / 変異: S218A S222A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MAP2K1, MEK1, PRKMK1 / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: Q02750, mitogen-activated protein kinase kinase
#2: タンパク質 Serine/threonine-protein kinase B-raf / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1


分子量: 31826.807 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: BRAF, BRAF1, RAFB1 / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: P15056, non-specific serine/threonine protein kinase

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非ポリマー , 6種, 333分子

#3: 化合物 ChemComp-A1AHE / N-[3-fluoro-4-({7-[(3-fluoropyridin-2-yl)oxy]-4-methyl-2-oxo-2H-1-benzopyran-3-yl}methyl)pyridin-2-yl]-N'-methylsulfuric diamide


分子量: 488.464 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C22H18F2N4O5S / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物 ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP


分子量: 506.196 Da / 分子数: 3 / 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
#5: 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
#6: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 11 / 由来タイプ: 合成 / 式: C2H6O2
#7: 化合物 ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 314 / 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: 2.62 Å3/Da / 溶媒含有率: 53.12 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8
詳細: 0.24 M di-ammonium hydrogen phosphate pH 8.0, 20% 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: Diamond / ビームライン: I03 / 波長: 0.97629 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2023年7月6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: 0.97629 Å / 相対比: 1
反射解像度: 2.07→58.52 Å / Num. obs: 83556 / % possible obs: 99.2 % / 冗長度: 7.1 % / Biso Wilson estimate: 39.54 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.6
反射 シェル解像度: 2.07→2.11 Å / Rmerge(I) obs: 0.709 / Num. unique obs: 2636

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
DIALSデータ削減
DIALSデータスケーリング
PHASER位相決定
REFMAC5精密化
精密化構造決定の手法: 分子置換 / 解像度: 2.07→41.2 Å / SU ML: 0.28 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 27.271
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.248 4072 4.92 %
Rwork0.213 78704 -
obs0.2147 82776 99.08 %
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: 59.81 Å2
精密化ステップサイクル: LAST / 解像度: 2.07→41.2 Å
タンパク質核酸リガンド溶媒全体
原子数8730 0 215 314 9259
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0039140
X-RAY DIFFRACTIONf_angle_d0.557412378
X-RAY DIFFRACTIONf_chiral_restr0.04351383
X-RAY DIFFRACTIONf_plane_restr0.00421560
X-RAY DIFFRACTIONf_dihedral_angle_d15.0273316
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.10.37521560.30822636X-RAY DIFFRACTION98.34
2.1-2.120.33421240.29392706X-RAY DIFFRACTION98.2
2.12-2.150.30611420.2712685X-RAY DIFFRACTION98.85
2.15-2.180.30971240.26622673X-RAY DIFFRACTION98.14
2.18-2.210.29521560.27352674X-RAY DIFFRACTION99.12
2.21-2.240.31691370.29682702X-RAY DIFFRACTION98.2
2.24-2.270.34411530.34222639X-RAY DIFFRACTION97.28
2.27-2.310.3281480.27072661X-RAY DIFFRACTION98.6
2.31-2.340.31351410.25452695X-RAY DIFFRACTION97.83
2.34-2.390.31451400.2542700X-RAY DIFFRACTION99.34
2.39-2.430.29061180.26092707X-RAY DIFFRACTION98.3
2.43-2.480.30651300.25652711X-RAY DIFFRACTION99.82
2.48-2.530.31251320.25312712X-RAY DIFFRACTION98.82
2.53-2.580.30141280.2512718X-RAY DIFFRACTION98.68
2.58-2.640.26741490.2422697X-RAY DIFFRACTION99.75
2.64-2.710.26731430.242699X-RAY DIFFRACTION99.16
2.71-2.780.31271530.23582711X-RAY DIFFRACTION99.13
2.78-2.860.2681390.24062725X-RAY DIFFRACTION99.27
2.86-2.950.26791400.25172722X-RAY DIFFRACTION99.34
2.95-3.060.30991440.24462715X-RAY DIFFRACTION99.44
3.06-3.180.29991250.23412732X-RAY DIFFRACTION99.65
3.18-3.330.25451550.22642729X-RAY DIFFRACTION99.69
3.33-3.50.23891500.21742719X-RAY DIFFRACTION99.65
3.5-3.720.2281300.20442753X-RAY DIFFRACTION99.76
3.72-4.010.24271390.18792755X-RAY DIFFRACTION99.69
4.01-4.410.19551630.1562722X-RAY DIFFRACTION99.9
4.41-5.050.1751450.15782770X-RAY DIFFRACTION99.93
5.05-6.360.20981400.18782779X-RAY DIFFRACTION99.93
6.36-41.20.20191280.1772857X-RAY DIFFRACTION99.63
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)
13.93075425555-2.179387332630.1241683790123.32555634110.3711013275821.283569773780.5877574592450.5169705185710.126228655985-0.592826504207-0.1558401406370.0241199221438-0.447179081685-0.392636966888-0.1658462090360.8710605107760.3766029190530.5169494761791.004126143680.638939258371.6914719833-5.8756451281124.7331147421-57.1122114655
22.7180592791-0.415518588921.808066453411.446951338820.7886916320412.07062601073-0.03508055578780.456836625621-0.0395260136250.1521550753910.349590917550.8868467000210.0391858792445-0.747953917226-0.345279061810.406614332637-0.0661234728614-0.08379770338240.948356794820.382251762830.872850165257-10.24207393693.1553323235-56.3640448697
30.473284901331-0.480381084340.7652852115182.49817280718-0.1920943720631.422520029470.5326056621810.5221116875390.9650447134430.6221096629210.3920559441271.01155847171-0.492167606715-1.058768356170.125345599580.5263317189860.1332146324370.4063892285140.6002954937470.2940974359851.10744156414-8.269350430977.8619856844-44.3206134632
43.460668160261.14606472131-0.6226393062252.04201547359-1.21296117592.199616374720.07330280739110.3593656210160.2175670241570.1631386748910.5326357395290.741555993493-0.0157863366279-0.353603751285-0.5154123206650.2832637617530.0569168106118-0.01503209506830.4593511171830.1776313688620.5685387008215.128591803917.08169035322-57.3825246167
51.857725569890.619445691095-0.1079887410631.06425233204-0.2216295298950.05969622459950.754028310470.1417893177530.9622945473620.6422581031810.2086018471280.827862604498-0.776451711681-0.259974376339-0.5290295159280.5371071235550.02541780804720.3186707416310.3716568301240.08898676929210.6309413605727.8590724849417.222602753-50.0116352686
65.561825663780.9757038247480.230472087081.68678362592-0.04835596136671.238344950740.784495912298-0.2320428363470.5335941815950.88689029471-0.32864198220.365409303124-0.4541762933050.121815762435-0.3838874535870.693874567699-0.1556224917440.1887225223660.387625914144-0.04930952345360.4710935396017.636215477985.87018430517-38.5568934443
71.339516157440.5309068398220.2529074363370.3626715656380.2226101236592.832589072320.532313443624-0.2205819856320.2389425447640.624189107287-0.3777080254330.270766826338-0.5722177036160.465475039546-0.1656232480030.546216352165-0.2247202011910.1297463398530.431860375319-0.07613566083430.35075548204221.85561636911.9509400151-45.4126715095
85.675037408333.05583030881.02554475169.812071630191.706884236916.653038139260.2248290969070.5591175631370.685305957194-0.06212119365280.1306421451330.938885718518-0.642764015591-0.125572078843-0.2762665479530.3216765644780.06392847537150.1609378644340.3609404428650.1329861852970.42138486569413.151888182319.2011468426-63.4925692991
98.605499993041.42460294048-1.028865816555.50978900587-0.8576498121927.55432541047-0.224210797755-1.26571513577-1.305212183760.306630793576-0.112964940707-0.8091147555080.5140097185190.4772012308790.3456487704850.3703656021040.0104678206005-0.08724875634790.5213989170490.1703394945420.667227549012-1.8557449210738.2812881635-22.9555560512
104.136409855131.637073695561.608615946712.142026418611.186575430825.727277281120.0821359021052-0.0753818698754-0.815890883125-0.218753787663-0.167512151836-0.6371364066831.172006532670.1243953862320.03008348913920.630453315817-0.04387826805880.0424101700380.4066440897910.04002352181630.509352546098-5.6838676936132.4947480349-30.0501580746
115.631390311051.3312668875-1.78844584922.76792570631-0.05557700278182.20643488609-0.0833093473649-0.2635032974430.1149032642410.0974299365053-0.05136721523320.1406380334090.161417246147-0.02809589560770.1192467960870.360230643153-0.125527484348-0.03383374208680.308272994336-0.01620238216390.292618910098-19.114107458243.0557529415-29.1704958999
124.673616165851.784095664350.4108682628736.24759936892-3.608744508372.59000192685-0.09123414437960.421188099551-0.4467476833460.416985791912-0.4135361967540.3833544347131.19368093645-0.1711286258320.431253420360.371594866781-0.1547441262860.0438887581480.416776644405-0.06052129863940.397285616516-17.794048724333.5730620186-36.884986143
132.6166027892.047902172640.07777110159073.094108018480.07791399202521.47196830196-0.2818932554790.2786609753060.12082412302-0.1040361380050.2638816439060.0800052384090.508557002423-0.2842554503820.02820421483550.479843255269-0.259688312526-0.01522547706910.506198834968-0.05519219113840.405109302043-32.347220617229.7237223438-32.4915100359
142.130109100011.44955711422-0.1302459620782.911905419350.09661966982191.89577780752-0.4370917876760.5994953725930.589841769938-0.5655178453440.2039906739591.049911400660.158488094807-0.5441064537560.2241672892670.388767350318-0.221974262138-0.1535065873180.6660793739910.01733439047990.702520031291-39.222170990837.607554161-36.7502845862
151.584024530910.101966212606-1.511059557561.583104416361.342838415674.550577980940.07156279612780.01993576833070.804044767751-0.42163116759-0.4608778768920.852783226334-0.925274901782-0.3354502125930.4900470172650.671461967206-0.348965290612-0.3346791667950.7173250076470.09382688741440.836303213051-32.49399488351.3456007052-40.8781854225
164.419315517770.927179262841-1.371610310341.727771134870.528217745160.863618279348-0.520334515681-1.25825126333-0.3790360991940.575550484357-0.0556534179354-0.4993170392330.7083529639820.0418345616060.2964700153021.80542128059-0.227727165677-0.3838161345111.267788256680.2387299285950.676609153388-27.8290037824.422005771726.61371781775
176.00160246826-1.3725471312-1.629283308083.88241584871-0.1379664286595.271845643060.245894634242-0.5135576527670.4506855769240.5813550000820.564737714272-1.229414683840.02205998545221.07606924063-0.6828935341430.80284080523-0.123148122123-0.3585901200250.648061896322-0.02069048518670.885424686286-14.768576813719.0597155768-2.50168999486
182.212243075840.00432106586964-0.1853310411454.01864534399-0.5680207880882.083322886330.415490021909-0.541133071169-0.3359019205920.955745328884-0.266954754439-0.5846102790130.778484434709-0.0901686700769-0.1133328932861.11805735563-0.290187005982-0.2187434694130.5878653847650.06545938968390.47776668672-27.929598166112.7626328396-8.17334697437
190.408890008512-0.08617816617630.7127441408485.460137738133.565786373545.45950628280.0490691677179-0.1483840010810.1009258131110.2730572180170.079926858018-0.07772013028780.385610388158-0.19183573036-0.1563360002380.666294416949-0.3388178265070.03615372920720.587584879358-0.02186013247440.382224164833-35.1009062817.9020717029-19.58577612
202.325413228760.9386836397780.08754285234661.32795414913-0.8637553223961.1054449208-0.05370510358890.310790792958-0.50397305950.1735509473470.12624173784-0.4355039097630.933319614505-0.271407314216-0.0581718729621.01704810938-0.3537386881180.02576607331920.471381431042-0.0983183143880.509531670634-32.98488864667.03870032848-27.3967076372
211.115079462280.24075634168-0.1947982448980.7563316060890.5802568674320.877880206762-0.0314206972946-0.176905472371-0.7906895766430.907405913083-0.0311081495283-0.3470622195171.35645245308-0.1484566049080.1417061057691.67928020183-0.511501515761-0.08133296421080.5055434763630.0423334053450.729896560423-36.3817579593-4.631609812-18.2551670793
227.97301400910.0876841739922-1.1319809152.12241500003-1.141619186882.18159974560.1182379070630.5341165403490.356314838069-0.3953160686880.09153021786610.0603559996920.107600148861-0.481443406273-0.212135488320.345541885424-0.0688151636935-0.009615458811250.428170504089-0.006159607293850.265510483432-7.32972431511-23.6409666822-47.3407248926
232.481487754491.15825569511-0.7876493086593.80024211990.9152433598942.12517313610.183836143877-0.1023883852910.1001968568060.223345377812-0.1177187587520.165373776388-0.121632471405-0.170537338679-0.05984887669740.259239124687-0.09641522119350.02190624460510.360794294160.02160062195670.326700918086-6.64928409429-22.1111434946-31.2336484162
241.109695472591.26370019497-0.2891807224013.238440166390.1034719410132.346249891770.398032640825-0.4243579177710.03292966244660.485061567269-0.294011170454-0.202044294363-0.3918786982420.3705065857-0.1023730424450.391165464506-0.209873425044-0.0372071320350.47313607580.001099374542170.3227902868477.47583609378-14.9028259566-29.4141409924
255.17883114907-1.390796163012.898771878438.882212739880.6820113669711.872270396380.285244300177-1.47585590177-0.05756130416661.62065003722-0.305739918004-0.05087643233070.3586757113930.35525314166-0.006061832975810.637505108732-0.309189490376-0.1187955219190.7222184749580.1038123535140.409340372633.46161529839-25.2098412285-14.7695219616
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
11(chain A and resseq 41:59)AA41 - 591 - 19
22(chain A and resseq 60:92)AA60 - 9220 - 52
33(chain A and resseq 93:137)AA93 - 13753 - 97
44(chain A and resseq 138:162)AA138 - 16298 - 122
55(chain A and resseq 163:206)AA163 - 206123 - 166
66(chain A and resseq 207:241)AA207 - 241167 - 201
77(chain A and resseq 242:358)AA242 - 358202 - 276
88(chain A and resseq 359:383)AA359 - 382277 - 300
99(chain B and resseq 449:475)BC449 - 4751 - 21
1010(chain B and resseq 476:507)BC476 - 50722 - 53
1111(chain B and resseq 508:587)BC508 - 58754 - 133
1212(chain B and resseq 588:614)BC588 - 614134 - 154
1313(chain B and resseq 615:670)BC615 - 670155 - 210
1414(chain B and resseq 671:706)BC671 - 706211 - 246
1515(chain B and resseq 707:722)BC707 - 721247 - 261
1616(chain C and resseq 41:59)CD41 - 595 - 23
1717(chain C and resseq 60:92)CD60 - 9224 - 55
1818(chain C and resseq 93:206)CD93 - 20656 - 169
1919(chain C and resseq 207:241)CD207 - 241170 - 204
2020(chain C and resseq 242:319)CD242 - 319205 - 240
2121(chain C and resseq 320:383)CD320 - 378241 - 299
2222(chain D and resseq 449:507)DF449 - 5071 - 59
2323(chain D and resseq 508:569)DF508 - 56960 - 121
2424(chain D and resseq 570:706)DF570 - 706122 - 258
2525(chain D and resseq 707:722)DF707 - 720259 - 272

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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