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- PDB-9axh: Crystal structure of KSR1/MEK1 complex heterotetramer with NST-628 -

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基本情報

登録情報
データベース: PDB / ID: 9axh
タイトルCrystal structure of KSR1/MEK1 complex heterotetramer with NST-628
要素
  • Dual specificity mitogen-activated protein kinase kinase 1
  • Kinase suppressor of Ras 1
キーワードTRANSFERASE / Inhibitor / complex / SIGNALING PROTEIN
機能・相同性
機能・相同性情報


regulation of MAP kinase activity / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / JUN kinase kinase activity / regulation of axon regeneration / mitogen-activated protein kinase kinase / placenta blood vessel development / MAP-kinase scaffold activity / labyrinthine layer development / cerebellar cortex formation ...regulation of MAP kinase activity / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / JUN kinase kinase activity / regulation of axon regeneration / mitogen-activated protein kinase kinase / placenta blood vessel development / MAP-kinase scaffold activity / labyrinthine layer development / cerebellar cortex formation / type B pancreatic cell proliferation / Signaling by MAP2K mutants / positive regulation of axonogenesis / regulation of Golgi inheritance / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / MAPK3 (ERK1) activation / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / endodermal cell differentiation / face development / MAP kinase kinase activity / Bergmann glial cell differentiation / Uptake and function of anthrax toxins / thyroid gland development / protein kinase activator activity / positive regulation of protein serine/threonine kinase activity / Schwann cell development / keratinocyte differentiation / 14-3-3 protein binding / myelination / ERK1 and ERK2 cascade / protein serine/threonine/tyrosine kinase activity / insulin-like growth factor receptor signaling pathway / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / thymus development / Signal transduction by L1 / cell motility / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / ruffle membrane / neuron differentiation / chemotaxis / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cellular senescence / Signaling by BRAF and RAF1 fusions / MAPK cascade / late endosome / regulation of cell population proliferation / heart development / protein tyrosine kinase activity / scaffold protein binding / Ras protein signal transduction / eukaryotic translation initiation factor 2alpha kinase activity / early endosome / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / positive regulation of ERK1 and ERK2 cascade / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of MAPK cascade / ciliary basal body / negative regulation of cell population proliferation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / centrosome / positive regulation of gene expression / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / endoplasmic reticulum / Golgi apparatus / signal transduction / protein-containing complex
類似検索 - 分子機能
Kinase suppressor RAS 1, N-terminal helical hairpin / Kinase suppressor RAS 1, N-terminal helical hairpin superfamily / Kinase suppressor RAS 1 N-terminal helical hairpin / : / : / 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 ...Kinase suppressor RAS 1, N-terminal helical hairpin / Kinase suppressor RAS 1, N-terminal helical hairpin superfamily / Kinase suppressor RAS 1 N-terminal helical hairpin / : / : / 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 / Sterile alpha motif/pointed domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 / Dual specificity mitogen-activated protein kinase kinase 1 / Kinase suppressor of Ras 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: 2.81 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: Dual specificity mitogen-activated protein kinase kinase 1
C: Kinase suppressor of Ras 1
D: Kinase suppressor of Ras 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)137,30017
ポリマ－134,0684
非ポリマー3,23213
水18010
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13610 Å2
ΔGint-119 kcal/mol
Surface area45970 Å2
手法PISA
単位格子
Length a, b, c (Å)249.870, 67.080, 74.400
Angle α, β, γ (deg.)90.000, 90.250, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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 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: 34575.836 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: 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 Kinase suppressor of Ras 1


分子量: 32458.354 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: KSR1, KSR / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: Q8IVT5, non-specific serine/threonine protein kinase

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非ポリマー , 6種, 23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: 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
#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: 4 / 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: 1 / 由来タイプ: 合成 / 式: C2H6O2
#7: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cl
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 10 / 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: 2.33 Å3/Da / 溶媒含有率: 47.1 %
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 / pH: 7 / 詳細: 0.1M SPG buffer pH 7.0, 25% w/v PEG 1500

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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: 2.81→52.24 Å / Num. obs: 30392 / % possible obs: 99.9 % / 冗長度: 6.9 % / Biso Wilson estimate: 85.77 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18
反射 シェル解像度: 2.81→2.91 Å / Rmerge(I) obs: 0.67 / Num. unique obs: 2553

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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
XDSデータ削減
XDS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: 2.81→52.24 Å / SU ML: 0.3919 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 27.4532
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2533 1567 5.17 %
Rwork0.2031 28758 -
obs0.2057 30325 99.8 %
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: 92.53 Å2
精密化ステップサイクル: LAST / 解像度: 2.81→52.24 Å
タンパク質核酸リガンド溶媒全体
原子数8241 0 202 10 8453
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00418619
X-RAY DIFFRACTIONf_angle_d0.62711730
X-RAY DIFFRACTIONf_chiral_restr0.04271318
X-RAY DIFFRACTIONf_plane_restr0.00481488
X-RAY DIFFRACTIONf_dihedral_angle_d14.94493004
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.90.41351530.32222553X-RAY DIFFRACTION99.63
2.9-30.34531420.27012585X-RAY DIFFRACTION99.63
3-3.120.30491300.26452621X-RAY DIFFRACTION99.71
3.12-3.270.31491110.28332612X-RAY DIFFRACTION99.71
3.27-3.440.33061240.25312587X-RAY DIFFRACTION99.71
3.44-3.650.30271340.22672632X-RAY DIFFRACTION99.78
3.65-3.930.24681620.212612X-RAY DIFFRACTION99.93
3.93-4.330.23611550.17812583X-RAY DIFFRACTION100
4.33-4.960.22051580.17492623X-RAY DIFFRACTION100
4.96-6.240.23391610.20092635X-RAY DIFFRACTION100
6.24-52.240.22721370.17532715X-RAY DIFFRACTION99.72
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)
13.837016744371.37495524087-0.275708623953.708030848240.8093891383983.05122096133-0.175307615371.55860151088-0.418002203003-0.4572361255630.288620737115-0.213864821751-0.5309428252860.0970752288358-0.1320012646411.01935393356-0.101370596444-0.03834923868091.4401803404-0.08225151978480.71440361806196.918349686815.8214246629-75.0623156426
24.75840877629-1.22155063357-0.1852098813155.571323803461.791427059434.28177114224-0.2997197802360.79533240874-0.0351835575396-0.2893000642980.2676851809970.494524819273-0.779336193496-0.615982347006-0.02170946822820.7888108982350.0389961170705-0.08278411760680.9734467195530.09380306821310.5250921817190.179703322417.270206449-63.49458798
35.60004112074-1.290361759871.455439522143.444745974650.7381507937968.615147714690.0406266792461.02693950131-0.157504517355-0.01162896420610.1830578809070.02904817039280.1344234096140.539647301156-0.2107501371080.650637810776-0.1154564113180.06829896370110.749759801772-0.08844833273820.448979427156104.54400346912.7970392693-62.898951649
42.08607909391-3.49508923466-3.944262279667.968559807555.728847908228.32950696739-0.664900110512-1.72508814307-0.8109297739160.0002108915570490.5282703173440.924574227890.5344741378610.006328158758860.2140418375720.8335604347080.05359329502260.00965995345410.9447011294430.1280622853480.75275143574995.618070128720.582889435-53.1852794157
54.45934168497-0.277877338718-1.343713469811.02397188274-0.1660265149488.2821140526-0.263420490467-0.105934083154-0.3605099884660.3175195591810.0826952379711-0.1918177491240.5565408008451.027011606610.1803994410810.7217361800710.09820593047940.02765898332880.702562090914-0.08889194344680.628920565808108.54768849410.8530807132-44.5101586135
64.58733556478-1.27787638656-1.300892035371.566632488342.261809904087.51543032362-0.03128777541770.613452745556-0.4809007038120.01364487833420.429455169264-0.3555845394420.8784437530471.88057753554-0.4504957342840.8196790001130.1582553881370.06264068181391.20604389477-0.1976888889060.938317546891119.7174834788.68973154838-56.225610182
75.461838782050.2305548236261.168205957094.28845917091.0518577617.42629566678-0.0960439021848-0.241649145716-0.4550732631590.0755696546978-0.1384299665550.180360370355-0.0804945388907-0.412996296940.1434344302540.5408171090880.103667152343-0.01125329162870.497794545701-0.01287388957230.6107581587118.061688447.540228336363.68939022868
84.65311148380.3224105088910.6149300140584.162425455192.665903793845.716007451720.0190864052551-0.0816592596758-0.36261509183-0.254960410857-0.0954295059546-0.161235714015-0.0585017649105-0.3398686475470.06436127356870.4906325797850.09516662812370.02350041642480.4948656849390.1164391854460.55180216414416.587170203911.87174720449.38694042691
90.5906044495831.177162154880.2854000819142.763219531780.7460029751960.540788924945-0.1900112525820.0763079006433-0.498685407031-0.263933563590.338536360225-0.289917660577-0.003433700030840.324631525501-0.2039180432550.7749703285090.102901157030.1028802240490.732796849590.1199432330580.9077597987630.508412454415.623883309711.7710310301
105.3110637261-0.2243110585110.1586758047843.892621843210.8646464569431.70004719474-0.0843658377099-0.7773799599770.4286502536820.317028845308-0.0700309275972-0.0978321503113-0.523551841213-0.3509018123560.1865451773230.7115036218210.165013567820.01871721905270.637121876465-0.02465616461490.53204249987520.445946798126.538058565822.4650977417
115.187299902131.53432863559-1.76982946091.95528205622-0.5641637330890.56928299488-0.37848173771-0.184678488202-0.185588611365-0.5402053591190.296231548713-0.324589440820.6782314155440.670151390887-0.09800392623751.15632231249-0.16081040766-0.09852281306661.8724203585-0.3831605291070.91260702064766.102833295111.1914758198-38.6378571212
121.70954226784-2.12692546474-1.159676263192.682884622031.312542081381.217742719270.6964909217830.9320235345350.45918455427-0.449648117154-0.557689503781-0.392337640312-1.4758126938-0.66544806097-0.0929066924631.156153144440.1856463844560.02327787486270.9749962651630.2108352972921.0840048407548.305615533625.3967443502-19.6733885808
134.15183701121.36178727524-2.406185219113.656679919220.4395240049733.59098180011-0.154317229610.612396759661-0.530129514399-0.03523554122670.126726727062-0.2181723652910.0812522167964-0.3713857723210.03108174644770.413164127855-0.025434571062-0.04057509067090.325984799215-0.01213369863440.71140193727356.800395058812.0180761873-8.89734338879
140.3481311758890.470572416703-0.8160237778991.09001598069-1.174549551953.954839872430.0892200581920.0193861916895-0.765990427418-0.2386168218-0.5121383227460.760805201119-0.8094700805-0.5971972468730.2921691971360.8371770293840.0845029969717-0.1289473903320.8743977281090.07478043182261.0844713857841.896050782722.1828661828-7.76293425046
155.77787682676-0.581784896066-2.246949021990.7718484743551.336087874672.78045286835-0.08417071940810.1582540463210.2536225454320.2513152821730.186359191770.496866765818-0.188295717322-0.548137706931-0.03276981351480.524416078130.0190744340579-0.02351385407560.3753059039210.1126198893490.67223742028646.774597926220.06461400674.19572588023
166.90704015936-3.55263724426-2.276320787172.75720342351.798223794911.1219034305-0.583265590458-1.25559822510.4701584141881.174840862050.668979843408-0.4212652344280.5298336776240.5482460051490.05102172136710.9470285972410.145908627851-0.1992795558480.618409823420.03519001426120.86925163420856.614480785115.97187578514.669316322
174.74795962582-0.953790976465-1.414197737172.435758558230.8624163604214.464356997850.0218528025439-0.01084539966080.8083964940870.2383187670920.209623218029-0.956048909607-0.09392081442920.422379009603-0.2172862601140.614192023073-0.0445537748207-0.1074429792910.485553152894-0.02915628733190.92048228748963.246475193521.50935464885.93112188484
186.149254086740.373613069308-3.43457548332.84883574632-1.738564545345.709265089790.1950382018640.6367763164860.0406081360044-0.4454660891760.3033768695090.230854011834-0.152267442907-0.315517018277-0.1992868965291.04912109405-0.275213937807-0.1476418907411.24476505734-0.06354285798261.208103030645.61876728410.8684114152-21.7097063523
193.1724635962-0.947499185285-1.200602773891.71125470584-0.5528314933120.945087016995-0.460556803554-0.530946569771-0.2813241531711.18594199599-0.2682785084690.5309506062320.316606612141-0.3706628119910.5599398174891.22044452187-0.155893994670.05224721805910.993975801139-0.007460029479190.9456881604970.66069396484.13135394463-28.8171367158
208.66233763917-1.19662223383-2.993090287670.978632771074-0.3051100533276.743497063470.07508579497121.156385974060.757550904662-0.3458656417420.02534711744720.4990315395460.0204060708969-0.541442468075-0.09834093669220.6314706431240.0343063791885-0.1032256314450.7337448082490.07079697940720.58779420211674.943971539120.4858651551-27.0594010483
218.82089448611-1.13312021913-5.477462281290.649445473309-0.1736965140314.56311515914-0.3341905712771.18034351993-0.483186065691-0.4810891078340.0308149216602-0.253303506734-0.385974301417-0.9877461513040.5802452142661.11786433059-0.3914449676890.03480535311581.07737823602-0.1702896607120.80689917239282.780940200610.3368235171-34.4851672325
225.81354017657-0.0553594821382-3.241989073930.457680777605-0.482385230962.55271552616-0.2614659459340.536399212775-0.311759834643-0.3101227162330.109802784159-0.07893282985540.250342211504-0.1692204013710.05503233334920.810227816669-0.0193540815284-0.01895342518170.666996340596-0.0873550858080.53195393184491.991492604916.3960717015-31.643386359
238.66576942449-0.741082843856-3.902415405841.761793235411.827863820146.075774219420.380147015192-1.665515525120.666551093626-0.06580577411290.04672317071950.282070685469-0.3578764120321.09098739509-0.3906007940740.735441897773-0.0857597721036-0.003956507526450.840768662682-0.162091897170.4638929399893.842306605524.535835834-20.3479075002
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 43:73)AA43 - 735 - 35
22(chain A and resseq 74:120)AA74 - 12036 - 82
33(chain A and resseq 121:206)AA121 - 20683 - 168
44(chain A and resseq 207:222)AA207 - 222169 - 184
55(chain A and resseq 223:319)AA223 - 319185 - 238
66(chain A and resseq 320:382)AA320 - 381239 - 300
77(chain B and resseq 38:92)BC38 - 921 - 55
88(chain B and resseq 93:206)BC93 - 20656 - 169
99(chain B and resseq 207:241)BC207 - 241170 - 204
1010(chain B and resseq 242:382)BC242 - 381205 - 300
1111(chain C and resseq 613:635)CE614 - 6351 - 22
1212(chain C and resseq 636:663)CE636 - 66323 - 48
1313(chain C and resseq 664:748)CE664 - 74849 - 133
1414(chain C and resseq 749:772)CE749 - 772134 - 150
1515(chain C and resseq 773:834)CE773 - 834151 - 212
1616(chain C and resseq 835:859)CE835 - 859213 - 237
1717(chain C and resseq 860:881)CE860 - 881238 - 259
1818(chain D and resseq 613:635)DF613 - 6351 - 23
1919(chain D and resseq 636:663)DF636 - 66324 - 44
2020(chain D and resseq 664:748)DF664 - 74845 - 129
2121(chain D and resseq 749:772)DF749 - 772130 - 140
2222(chain D and resseq 773:834)DF773 - 834141 - 202
2323(chain D and resseq 835:881)DF835 - 881203 - 249

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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