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- PDB-8fy2: E3:PROTAC:target ternary complex structure (VCB/WH244/BCL-2) -

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基本情報

登録情報
データベース: PDB / ID: 8fy2
タイトルE3:PROTAC:target ternary complex structure (VCB/WH244/BCL-2)
要素
  • Apoptosis regulator Bcl-2
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
キーワードTRANSCRIPTION / ternary complex / degrader
機能・相同性
機能・相同性情報


negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / channel inhibitor activity / melanin metabolic process ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / channel inhibitor activity / melanin metabolic process / positive regulation of neuron maturation / myeloid cell apoptotic process / cochlear nucleus development / osteoblast proliferation / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / stem cell development / gland morphogenesis / renal system process / regulation of cell-matrix adhesion / ear development / The NLRP1 inflammasome / dendritic cell apoptotic process / negative regulation of calcium ion transport into cytosol / regulation of cellular response to hypoxia / lymphoid progenitor cell differentiation / melanocyte differentiation / T cell apoptotic process / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / regulation of nitrogen utilization / glomerulus development / focal adhesion assembly / negative regulation of T cell apoptotic process / regulation of transmembrane transporter activity / oocyte development / B cell apoptotic process / metanephros development / neuron maturation / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of multicellular organism growth / target-directed miRNA degradation / transcription elongation factor activity / negative regulation of motor neuron apoptotic process / elongin complex / regulation of viral genome replication / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / response to UV-B / calcium ion transport into cytosol / Replication of the SARS-CoV-1 genome / negative regulation of ossification / response to iron ion / VCB complex / axon regeneration / epithelial cell apoptotic process / Cul5-RING ubiquitin ligase complex / negative regulation of mitochondrial depolarization / motor neuron apoptotic process / positive regulation of smooth muscle cell migration / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of B cell apoptotic process / Cul2-RING ubiquitin ligase complex / organ growth / intracellular membraneless organelle / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / digestive tract morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / B cell lineage commitment / SUMOylation of ubiquitinylation proteins / pore complex / negative regulation of intrinsic apoptotic signaling pathway / T cell homeostasis / BH3 domain binding / B cell homeostasis / regulation of calcium ion transport / B cell proliferation / humoral immune response / negative regulation of anoikis / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of apoptotic signaling pathway / negative regulation of transcription elongation by RNA polymerase II / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / hematopoietic stem cell differentiation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand
類似検索 - 分子機能
Apoptosis regulator, Bcl-2 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Apoptosis regulator, Bcl-2/ BclX ...Apoptosis regulator, Bcl-2 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Elongin-C / Elongin B / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
類似検索 - ドメイン・相同性
: / Apoptosis regulator Bcl-2 / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
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: 2.98 Å
データ登録者Nayak, D. / Lv, D. / Yuan, Y. / Zhang, P. / Hu, W. / Ruben, E. / Lv, Z. / Sung, P. / Hromas, R. / Zheng, G. ...Nayak, D. / Lv, D. / Yuan, Y. / Zhang, P. / Hu, W. / Ruben, E. / Lv, Z. / Sung, P. / Hromas, R. / Zheng, G. / Zhou, D. / Olsen, S.K.
資金援助 米国, 6件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM115568 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM128731 米国
Cancer Prevention and Research Institute of Texas (CPRIT)RR200030 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA242003 米国
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA241191 米国
National Institutes of Health/National Institute on Aging (NIH/NIA)R01 AG063801 米国
引用ジャーナル: Nat Commun / 年: 2024
タイトル: Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL.
著者: Nayak, D. / Lv, D. / Yuan, Y. / Zhang, P. / Hu, W. / Nayak, A. / Ruben, E.A. / Lv, Z. / Sung, P. / Hromas, R. / Zheng, G. / Zhou, D. / Olsen, S.K.
履歴
登録2023年1月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年4月10日Provider: repository / タイプ: Initial release

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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: von Hippel-Lindau disease tumor suppressor
B: Elongin-B
C: Elongin-C
D: Apoptosis regulator Bcl-2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,4205
ポリマ－67,7394
非ポリマー1,6821
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)47.278, 102.604, 167.362
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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要素

#1: タンパク質 von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


分子量: 20729.531 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: VHL / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P40337
#2: タンパク質 Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


分子量: 13147.781 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ELOB, TCEB2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15370
#3: タンパク質 Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


分子量: 10843.420 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ELOC, TCEB1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q15369
#4: タンパク質 Apoptosis regulator Bcl-2


分子量: 23017.896 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BCL2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P10415
#5: 化合物 ChemComp-YFH / N-({4-[2-(4-{[(4R)-4'-chloro-4-methyl-6-{[4-(4-{[4-{[(2R)-4-[(1R,4R)-2-oxa-5-azabicyclo[2.2.1]heptan-5-yl]-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}-2,3,4,5-tetrahydro[1,1'-biphenyl]-4-yl]methyl}piperazin-1-yl)-2-oxoethyl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4S)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide


分子量: 1681.511 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C83H105ClF3N13O11S4 / タイプ: SUBJECT OF INVESTIGATION
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: 2.98 Å3/Da / 溶媒含有率: 58.66 %
結晶化温度: 291 K / 手法: 蒸気拡散法
詳細: 0.1 M Tris-Cl pH 8.7, 18% PEG 8000, 0.2 M MgCl2 and 3% 1,6-Hexanediol

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データ収集

回折平均測定温度: 108 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: 0.979 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2022年7月24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: 0.979 Å / 相対比: 1
反射解像度: 2.98→167.5 Å / Num. obs: 17444 / % possible obs: 100 % / 冗長度: 8.2 % / Biso Wilson estimate: 92.16 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.199 / Net I/σ(I): 11.5
反射 シェル解像度: 2.98→3.14 Å / Rmerge(I) obs: 2.21 / Num. unique obs: 2476

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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
精密化構造決定の手法: 分子置換 / 解像度: 2.98→83.68 Å / SU ML: 0.5468 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 32.222
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2786 1728 9.99 %
Rwork0.2294 15577 -
obs0.2344 17305 99.44 %
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: 96.21 Å2
精密化ステップサイクル: LAST / 解像度: 2.98→83.68 Å
タンパク質核酸リガンド溶媒全体
原子数3907 0 115 0 4022
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00224131
X-RAY DIFFRACTIONf_angle_d0.52055620
X-RAY DIFFRACTIONf_chiral_restr0.0387601
X-RAY DIFFRACTIONf_plane_restr0.0036718
X-RAY DIFFRACTIONf_dihedral_angle_d15.19391543
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.060.53691350.54361218X-RAY DIFFRACTION96.16
3.06-3.160.4181430.42621289X-RAY DIFFRACTION99.17
3.16-3.280.40021380.33871243X-RAY DIFFRACTION99.71
3.28-3.410.32131450.29921305X-RAY DIFFRACTION99.66
3.41-3.560.34911410.28891271X-RAY DIFFRACTION99.86
3.56-3.750.33021420.28511276X-RAY DIFFRACTION100
3.75-3.990.35711440.27351303X-RAY DIFFRACTION99.79
3.99-4.290.29241460.19641306X-RAY DIFFRACTION99.52
4.29-4.720.25431430.17181301X-RAY DIFFRACTION99.86
4.73-5.410.19361460.18621309X-RAY DIFFRACTION99.93
5.41-6.810.26141480.22431342X-RAY DIFFRACTION100
6.81-83.680.2191570.17741414X-RAY DIFFRACTION99.56
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)
10.3111677321430.4446492964380.3741768277320.4977394589730.4931896006060.3614049262080.387970509658-0.1621319724840.06355723745510.15107937160.06448249860420.657714750918-0.1781077190250.383664428365-6.3860878426E-60.619417012696-0.02242902074870.009310090031680.5575043568070.1171374237430.6408553499467.06492379068-13.8032513637-17.6042195869
21.033619703390.979135634917-0.4688587607060.543186251318-0.4861636269080.0686404517902-0.2330593876840.222802989443-0.256892080570.09967211848290.02381123895780.103040923720.1821914237940.149765281854-7.2410868579E-60.6373440857440.02868959228050.01493097423680.8578006660920.06673621099960.532353106599.75741111442-16.4084739754-25.3240920548
30.2016870373750.322020859883-0.2595103414940.464230461757-0.4854743005470.366354970570.142509736592-0.179219364561-0.0995444985898-0.071804614248-0.323959807165-0.450830672892-0.8611192270030.83665434344-6.62304775021E-50.746999304238-0.0912893165164-0.02057453280380.977418795752-0.01711046789750.9067183456314.611916-10.0508289536-24.0429175291
40.205076942956-0.3488954062370.465006241743-0.173940722764-0.3939631516410.9488474126540.356313687097-0.385633876607-0.25621369832-0.373519092858-0.1932229510480.549488122034-0.5837585988430.817995501450.002866291541220.684881050855-0.06538649470650.0143105073720.6315556625030.1512837128990.97567871057820.2444700959-9.37513832973-31.59131682
50.1133202155370.01987418553930.06748770310440.403846629789-0.1958861162430.173233120629-0.01162081200850.238081132169-0.248901120558-0.4163826876760.275162480839-0.475328858032-0.07646978885750.06872239159115.05109717884E-50.7809177646090.0937464413343-0.07859453399780.825783542890.07102659029221.0163039251936.3730478789-24.3497864233-35.168195678
60.14886398298-0.2379791125620.004292910870080.8508819528780.6663889520750.694662815181-0.131542105093-0.812046633097-0.306694300373-0.339345923574-0.2065612911540.228619782386-0.9347158296690.964999198221-0.0166498270520.412765484629-0.0898946376603-0.1263513417751.074842014950.1160397026660.6114779921524.3580740207-15.3030110538-14.7872442732
70.4662316872220.1453998541360.02010460835430.406215886866-0.3984871930830.443025018585-0.199169840497-0.1265563031420.695950705649-0.5632427469620.340452721925-0.187592127821-0.164460750841-0.2173737369690.002239663312130.680255354121-0.08107774461730.06506042001150.4658357213970.001025603321440.64800062929832.669651468610.5294711936-46.7989174603
80.5991165563360.4513254321090.1613902299220.3896405788480.1674273212170.06910611092080.1949479306240.7043912855130.3483424507870.02011962187160.203561645212-0.07144043380640.1731734897840.04802324871590.0001014420849040.6617265351810.094383093941-0.06589606180990.5763160741710.01138886495930.74751828587638.268571584620.2351948437-49.9924527974
90.6080992207060.2618670608370.456836474850.89918657496-0.297944908441.614597345580.2262045162640.6902600191870.228843013326-0.2585822985031.235410662370.529769922693-0.38867702295-1.148845144240.6015347393890.747089486861-0.212503730748-0.02119159417440.7445411306060.216270689890.87245010493727.493460067316.0973001654-56.8268613551
100.08552786159050.09729136704870.01411382197350.104619248358-0.03852795027130.0289101362670.09455198800840.107082774270.648429185805-0.536975482868-0.246493522966-0.296787385817-0.717280495083-0.4980373538441.7858331898E-50.51530373901-0.068914000667-0.02877008093850.919739550983-0.01461379950290.61340960579824.22729822764.79165783281-47.0291144018
110.09897489049990.1184402276070.11000304130.0401765382808-0.05275316208850.115021357197-0.07614287374670.723035891651-0.513990991404-0.44008051139-0.220521304305-0.6861095792150.9109497398970.8139141100020.0001088616627660.647710822008-0.00916011329853-0.1196022460331.044542956330.009459196026180.55920291563837.365854759411.9132384535-53.7513424156
120.02575231937580.0325853477112-0.02096354386860.0250390190553-0.03145658572440.06680992571820.00725784195632-0.1692393853030.708729331489-0.3679864952060.0365743616821-0.3673607792190.3563365261520.6656985396270.001082375229471.006776215390.0132847790883-0.01378043646260.970549647671-0.08533069699480.93814806438947.804677903222.1677396768-61.5986207623
13-0.00888643186759-0.006788665711420.01227500958690.0288501039697-0.08378879021160.1108228739730.2683788410460.5377344795940.2913185096260.166427603226-0.332252494167-1.98760033427-0.8612937796370.0920357737529-7.14130100535E-50.9436456620140.1769030968430.2236548740520.7493155098970.1031504204760.71899965088942.361644038913.6775691793-60.9943814517
140.08804385545040.193380513443-0.01470091462510.138079423126-0.1773173316520.1718446356610.107207765703-0.436254391886-0.921644418835-0.778535985456-0.7791338765270.1059903799910.2577213709741.12202768082-0.005719273741110.9136063433140.1447092221010.2301721398330.7076312329580.04787355013690.75968992696241.0482035733-7.37650121856-53.3627403489
150.42063195572-0.168894560236-0.5868102895740.3963821891550.6432346879371.308939266970.763242760792-0.4024552057140.0471582288989-0.3260274289680.985780895394-0.264555130986-0.2792127810740.2871431761740.03905384616821.10363568508-0.0445955496147-0.1350427336690.5327130337770.05410837568810.95357497627633.8380532903-24.2911950485-49.0449740495
160.5724277073190.05562665898920.2491701497490.4761144196290.0439559834920.0266113027491-0.157202223160.38240739052-0.387669425294-0.419553568449-0.07055279988190.0474098975349-0.05578529240510.101173770973-7.0707970296E-60.590573792699-0.003206869372210.002175678791950.7328981116420.1515091140230.53732358865543.22953712014.40968200458-37.2449597881
170.3188565321480.4341891537980.10060060490.5741672442170.1660688556070.0313978463404-0.3416630653140.384692883498-0.314989329658-0.4546873230360.273977825905-0.2689976854490.135087381740.694397548790.01173635001290.559734061530.08713906391980.01098908389131.041026484120.3272611455570.74832052286949.3679484091-0.372190996152-39.0219874698
180.3344482897950.3837139710210.4915633512580.571522655990.2077014554270.6736134150270.667803812522-0.02905370321750.282912719675-0.388814654946-0.4727079909450.183224588337-0.770319219139-0.2316947077820.0001126503217220.7243439751860.1215989447890.1476559257160.8766026571490.08554580163260.64308311007629.561066792-1.56314385492-38.0789834009
191.287108776350.125671937981-1.110993426290.0603335110146-0.1399148491920.942094966452-0.704109106303-1.424788193210.483368741036-0.466812218345-0.2860907695410.172399233284-0.9463194315660.970094872309-0.02808030297010.5526419242450.06438040145030.042162938270.4881392232950.1898618823130.63455355989339.3641523538-10.931882459-38.6860078193
200.54752756259-0.08794300475610.08941376557260.0204957357817-0.0203680810588-0.05756341411270.4393771912560.0825946973198-0.4122241648310.753449244751.00391346931-0.550019891670.142066091769-0.4271993724940.8743518442491.2631577433-0.06790498700550.240009031240.9537837963530.2008768452990.93671834816-13.1145577192-48.0003087176-7.78766726127
210.342332511241-0.147393270824-0.4300315086270.1914427499360.1786011593170.213257714574-0.115591740658-1.1122541303-0.08303479495170.114070656320.5176395663040.329024354059-0.281141095406-0.1392608180720.00274229832271.15427201863-0.1239515567760.1138761840220.8941003005470.2160689815321.0486125679-14.0370844783-46.7326603657-2.21161213742
221.028613248160.07466719626850.419873795061-0.0117246021549-0.009598339324590.0514023469072-0.946983807198-1.200770847210.60755178324-0.1036228965170.60367717029-0.2029583106010.3948624595350.00732867056408-0.02322487079031.179361852490.1922516427360.04298201075711.036819541540.0701268143040.614295005841-2.14538974337-46.053373691-10.1724770144
230.288049559085-0.1565959728860.1528135103250.0626626195955-0.1336580359520.06314774485680.07095146653331.50136807103-0.519979443353-0.08134879859830.1675532037520.525982974261-0.2584219245490.2325533929010.003465655980840.8352103318420.05905257148970.08311984958730.509860447559-0.003804576859480.681165860684-6.66488015315-28.0196048262-9.01644966736
240.544197655373-0.1096649303-0.212880585003-0.004907591878310.0352678353205-0.0886986674489-0.4611533842041.38928472446-0.677151679463-0.5720568570110.2336390650161.128998732060.237118430483-0.1353578557480.003973313423630.8764385464520.034710696218-0.07370212394280.7241084835870.01818416920350.7629365232-15.7600681574-32.1193415303-18.6189978031
250.0747830764325-0.1419750219870.05972148119311.44521280246-0.3623524585790.07331440634760.1296195041970.0564115767907-0.203138065795-0.0893731053715-0.2116979838140.4907058689640.075043622207-1.201609296291.07602464195E-50.883164346527-0.2591971403490.1008350094231.043186092770.0297656654560.755670460717-15.9210151116-38.0977198512-10.6434192269
260.7184187899230.5288945414391.031098009220.4787758852330.7939332809591.535056275060.2759446841080.706890807436-1.08763903908-0.2889655007940.725234085196-1.373035388280.7303129471010.5640679441120.3747290951160.998900593407-0.5815260160150.3109696724191.42918470635-0.3793570002241.22789834264-12.6668853621-49.1820154206-25.9763672876
270.1055278589890.02188340920710.01301084222320.3240567698880.2543567704490.226129232003-0.0176499911719-0.194287527697-0.6461506858460.240522559681-0.123247451023-0.03478408812231.023408245930.07996131054080.02597192398061.671182569880.232980408450.2186076071050.5577695187220.1740826648711.02023926858-2.81932810143-52.2422840556-18.5413525345
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
11chain 'A' and (resid 60 through 79 )AA60 - 791 - 20
22chain 'A' and (resid 80 through 121 )AA80 - 12121 - 62
33chain 'A' and (resid 122 through 141 )AA122 - 14163 - 82
44chain 'A' and (resid 142 through 169 )AA142 - 16983 - 110
55chain 'A' and (resid 170 through 193 )AA170 - 193111 - 134
66chain 'A' and (resid 194 through 208 )AA194 - 208135 - 149
77chain 'B' and (resid 1 through 23 )BB1 - 231 - 23
88chain 'B' and (resid 24 through 45 )BB24 - 4524 - 45
99chain 'B' and (resid 46 through 60 )BB46 - 6046 - 60
1010chain 'B' and (resid 61 through 72 )BB61 - 7261 - 72
1111chain 'B' and (resid 73 through 79 )BB73 - 7973 - 79
1212chain 'B' and (resid 80 through 84 )BB80 - 8480 - 84
1313chain 'B' and (resid 85 through 89 )BB85 - 8985 - 89
1414chain 'B' and (resid 90 through 99 )BB90 - 9990 - 99
1515chain 'B' and (resid 100 through 105 )BB100 - 105100 - 105
1616chain 'C' and (resid 17 through 45 )CC17 - 451 - 29
1717chain 'C' and (resid 46 through 66 )CC46 - 6630 - 39
1818chain 'C' and (resid 67 through 96 )CC67 - 9640 - 69
1919chain 'C' and (resid 97 through 112 )CC97 - 11270 - 85
2020chain 'D' and (resid 8 through 25 )DD8 - 251 - 18
2121chain 'D' and (resid 26 through 90 )DD26 - 9019 - 28
2222chain 'D' and (resid 91 through 107 )DD91 - 10729 - 45
2323chain 'D' and (resid 108 through 122 )DD108 - 12246 - 60
2424chain 'D' and (resid 123 through 143 )DD123 - 14361 - 81
2525chain 'D' and (resid 144 through 184 )DD144 - 18482 - 122
2626chain 'D' and (resid 185 through 193 )DD185 - 193123 - 131
2727chain 'D' and (resid 194 through 203 )DD194 - 203132 - 141

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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