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- PDB-9h32: T2R-TTL-PROTAC3 complex -

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基本情報

登録情報
データベース: PDB / ID: 9h32
タイトルT2R-TTL-PROTAC3 complex
要素
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin--tyrosine ligase
キーワードCELL CYCLE / TUBULIN FOLD / CYTOSKELETON / MICROTUBULE
機能・相同性
機能・相同性情報


tubulin-tyrosine ligase / regulation of metaphase plate congression / tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / tubulin binding ...tubulin-tyrosine ligase / regulation of metaphase plate congression / tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / cellular response to interleukin-4 / tubulin binding / positive regulation of mitotic cell cycle / post-translational protein modification / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / growth cone / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / microtubule / neuron projection / cilium / protein heterodimerization activity / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol
類似検索 - 分子機能
: / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. ...: / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
類似検索 - ドメイン・相同性
: / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin--tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
類似検索 - 構成要素
生物種Rattus norvegicus (ドブネズミ)
Gallus gallus (ニワトリ)
Bos taurus (ウシ)
手法X線回折 / シンクロトロン / フーリエ合成 / 解像度: 2.31 Å
データ登録者Maiocchi, A. / Abel, A.-C. / Boiarska, Z. / Steinmetz, M.O. / Passarella, D. / Prota, A.E.
資金援助European Union, スイス, 2件
組織認可番号
European Union (EU)860070 TubInTrainEuropean Union
Swiss National Science Foundation31003A_166608 スイス
引用
ジャーナル: To Be Published
タイトル: Effective tubulin degradation by rationally designed Proteolysis Targeting Chimeras
著者: Maiocchi, A. / Abel, A.-C. / Basellini, M. / Perez Pena, H. / Boiarska, Z. / Ferrandi, E. / Kozicka, Z. / Fasano, V. / Pieraccini, S. / Cappelletti, G. / Steinmetz, M.O. / Prota, A.E. / Passarella, D.
#1: ジャーナル: Acta Crystallogr D Struct Biol / : 2019
タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
履歴
登録2024年10月15日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年10月29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: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin--tyrosine ligase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)265,64022
ポリマ-261,6316
非ポリマー4,00916
5,080282
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)105.030, 157.920, 181.430
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

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タンパク質 , 4種, 6分子 ACBDEF

#1: タンパク質 Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


分子量: 50204.445 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 器官: brain / 参照: UniProt: P81947
#2: タンパク質 Tubulin beta-2B chain


分子量: 49999.887 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 器官: brain / 参照: UniProt: Q6B856
#3: タンパク質 Stathmin-4 / Stathmin-like protein B3 / RB3


分子量: 16844.162 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Stmn4 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P63043
#4: タンパク質 Tubulin--tyrosine ligase


分子量: 44378.496 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Gallus gallus (ニワトリ) / 遺伝子: TTL / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A8V0Z8P0, tubulin-tyrosine ligase

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非ポリマー , 8種, 298分子

#5: 化合物 ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


分子量: 523.180 Da / 分子数: 2 / 由来タイプ: 合成 / : C10H16N5O14P3 / コメント: GTP, エネルギー貯蔵分子*YM
#6: 化合物
ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 5 / 由来タイプ: 合成 / : Mg
#7: 化合物
ChemComp-CA / CALCIUM ION


分子量: 40.078 Da / 分子数: 4 / 由来タイプ: 合成 / : Ca
#8: 化合物 ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 2 / 由来タイプ: 合成 / : C10H15N5O11P2 / コメント: GDP, エネルギー貯蔵分子*YM
#9: 化合物 ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


分子量: 195.237 Da / 分子数: 1 / 由来タイプ: 合成 / : C6H13NO4S / コメント: pH緩衝剤*YM
#10: 化合物 ChemComp-A1ISD / (1S,2R,3S,5S,6S,16E,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16-tetraen-6-yl 4-(2-{4-[4-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-4-yl}amino)-4-oxobutyl]-1H-1,2,3-triazol-1-yl}ethyl)benzoate


分子量: 1093.614 Da / 分子数: 1 / 由来タイプ: 合成 / : C56H65ClN8O13 / タイプ: SUBJECT OF INVESTIGATION
#11: 化合物 ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


分子量: 505.208 Da / 分子数: 1 / 由来タイプ: 合成 / : C11H18N5O12P3
コメント: AMP-PCP, エネルギー貯蔵分子類似体*YM
#12: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 282 / 由来タイプ: 天然 / : H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationN

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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: 2.88 Å3/Da / 溶媒含有率: 57.22 %
結晶化温度: 293 K / 手法: 蒸気拡散法 / pH: 6.5
詳細: 4% PEG 4K, 13% glycerol, 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine

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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: SLS / ビームライン: X06SA / 波長: 1.00003 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年5月2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: 1.00003 Å / 相対比: 1
反射解像度: 2.31→48.05 Å / Num. obs: 256190 / % possible obs: 99.9 % / 冗長度: 7.1 % / Biso Wilson estimate: 59.05 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.1139 / Rpim(I) all: 0.04562 / Rrim(I) all: 0.1228 / Net I/σ(I): 9.92
反射 シェル解像度: 2.31→2.33 Å / Rmerge(I) obs: 3.032 / Mean I/σ(I) obs: 0.47 / Num. unique obs: 8440 / CC1/2: 0.589 / Rpim(I) all: 1.214 / Rrim(I) all: 3.269

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21.1_5286精密化
XDSデータ削減
XSCALEデータスケーリング
PHENIX位相決定
精密化構造決定の手法: フーリエ合成 / 解像度: 2.31→48.05 Å / SU ML: 0.3477 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 26.7319
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2352 6638 5 %
Rwork0.2109 126101 -
obs0.2121 132739 99.83 %
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: 75.45 Å2
精密化ステップサイクル: LAST / 解像度: 2.31→48.05 Å
タンパク質核酸リガンド溶媒全体
原子数17325 0 250 282 17857
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.001517985
X-RAY DIFFRACTIONf_angle_d0.436824389
X-RAY DIFFRACTIONf_chiral_restr0.03892653
X-RAY DIFFRACTIONf_plane_restr0.00253156
X-RAY DIFFRACTIONf_dihedral_angle_d11.02226676
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.330.36322170.34694107X-RAY DIFFRACTION97.56
2.33-2.360.342170.33144133X-RAY DIFFRACTION99.95
2.36-2.390.36192190.32894176X-RAY DIFFRACTION99.98
2.39-2.420.36852180.35344136X-RAY DIFFRACTION100
2.42-2.450.37442200.36194186X-RAY DIFFRACTION99.98
2.45-2.490.33422180.31614139X-RAY DIFFRACTION99.98
2.49-2.520.33722210.33064184X-RAY DIFFRACTION99.59
2.52-2.560.34032200.30454181X-RAY DIFFRACTION99.98
2.56-2.60.30962180.28484157X-RAY DIFFRACTION100
2.6-2.640.30522190.27394164X-RAY DIFFRACTION99.98
2.64-2.690.32642210.2724186X-RAY DIFFRACTION100
2.69-2.740.28542190.27144162X-RAY DIFFRACTION99.95
2.74-2.790.3042210.27114200X-RAY DIFFRACTION99.91
2.79-2.850.30942200.27024179X-RAY DIFFRACTION99.93
2.85-2.910.27652190.27694166X-RAY DIFFRACTION99.95
2.91-2.970.30422200.28544178X-RAY DIFFRACTION99.95
2.97-3.050.32072210.27134207X-RAY DIFFRACTION99.93
3.05-3.130.27242210.2534189X-RAY DIFFRACTION100
3.13-3.220.23012210.2424205X-RAY DIFFRACTION99.98
3.22-3.330.26382220.23174209X-RAY DIFFRACTION99.95
3.33-3.450.2422200.22684181X-RAY DIFFRACTION99.84
3.45-3.580.27042210.21854211X-RAY DIFFRACTION100
3.58-3.750.22372230.20974223X-RAY DIFFRACTION99.57
3.75-3.940.19762220.18614214X-RAY DIFFRACTION100
3.94-4.190.20812220.17964234X-RAY DIFFRACTION100
4.19-4.520.18452240.16374246X-RAY DIFFRACTION100
4.52-4.970.19042250.15344269X-RAY DIFFRACTION100
4.97-5.690.21432250.18374284X-RAY DIFFRACTION100
5.69-7.160.23082260.19284299X-RAY DIFFRACTION99.45
7.16-48.050.17122380.15814496X-RAY DIFFRACTION99.58
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.42285808871-0.256276961405-0.871540578045.57961732606-1.038815879232.015507241310.129141728778-0.03727223436350.508598276779-0.5272477328380.191021008163-0.328523363982-1.215792263720.478647493625-0.3094544802960.926752902774-0.1660603403340.1832176129740.567215224345-0.1450459859250.52896650227829.152295091197.784004845354.0062409971
21.51914271028-0.111446685266-0.01865467786333.760590586131.768563126883.85213652717-0.01324627505790.1401707299710.079810050196-0.2397868770910.346655509839-0.448520474243-0.5347620696610.594857373835-0.325086400540.437415089921-0.07293767619180.06138023521920.477746506422-0.1437146187540.49373929806828.925742965682.480486155555.5782704746
31.797314859251.84686362618-1.046168200833.421474090631.697889560366.091099867050.0639297599022-0.1604193414540.009650948536050.55084087156-0.1057743061140.670811431526-0.236724963393-0.5429447132650.06088144233780.5328659892680.02123699507250.09626936405160.435971116674-0.1438850506750.52240845596814.056503223984.55124090470.7771683966
40.7358041509910.4969974980710.7312773977327.383305236840.2816559387610.755394522613-0.0918909161628-0.3341342657730.188864947690.9155290183820.2414886870570.45606295321-0.1867133518020.0757450992473-0.1074138753440.7298104855780.05607293277710.1147543018810.540219122357-0.1348129448340.52677169458317.235553179488.046605359680.1796564871
51.47435115979-0.769808144503-0.524019690545.431782481382.834170039413.98178192559-0.0401450483238-0.165674506141-0.05164132638560.8474542591720.215850362852-0.09904454119850.5033632774350.427124678224-0.1610208842510.393018016136-0.0323488274383-0.005245925207470.457530901244-0.09867959859260.49678298867124.416186827873.733333801967.4928424276
65.66477064861-2.18144652233-0.6818354174186.30254931782.449756516085.960957508410.1075001297450.4089665119690.728592436036-0.593650603457-0.2563431516710.314750851525-1.2184222106-0.4029769382760.1476747145690.5603222847660.0734218924840.01806764317840.4350585094340.02598801013140.55573712233516.199940699970.235577321619.2262396598
71.6237656109-0.662179132514-0.1820945647193.275271205651.330863514243.738424856250.01827674410130.1691142982530.0202387153805-0.0771838756666-0.06751495679190.0502093497404-0.194679395953-0.04839392303620.03485410591350.2944605792490.02610503575480.002952447752980.432199636754-0.1026711538840.45266587680620.353664805754.308893135323.3529835069
84.73062926473-2.293592340380.2956742844613.36655637682-0.7703099292343.54615823076-0.0224756906505-0.1303979494410.0951708491342-0.0571246905564-0.1065518635540.266990279393-0.24177928019-0.6512112715120.1281823769140.4265503422140.04196130807420.00158504625490.528064954573-0.2324118884590.47680890182510.828782573362.922208631538.4288352925
90.800261408669-0.543125693944-0.1125639048663.023447239552.04174550543.65513525738-0.119313266037-0.1303107116540.04372144379210.584168354257-0.1253309426310.3192211421670.303254744526-0.4598007389180.2244092405130.358895994241-0.05652678729360.03537708177250.509817032003-0.08869018245770.50830670564313.698353163350.851434342238.4747251865
101.42873419652-0.4642514783810.2236110203262.366034194870.04534815804882.19976153276-0.04832102634150.2103016501340.0903802989799-0.2377485550190.0751645741176-0.0295776837658-0.1378144183060.0982532156822-0.02050147539650.345646949271-0.05845890472150.01803666051970.445291335157-0.03767245393630.40934963706517.95995528931.7777447933-11.2978200665
112.11002019137-0.6641922255350.944864740080.9905703247270.6488934901613.43429294375-0.00965404366466-0.1071198826060.1547214787390.0731433005553-0.1324627800590.308215372859-0.0128396015059-0.601708933810.1548808293570.331610304827-0.04413663051950.0484775707710.413943635337-0.06837254170820.4757330905253.9399794431231.24170877782.36791840433
124.51845946888-1.836688384624.422451962332.5416873706-1.863563725466.36119340596-0.0733741762334-0.4485685777240.1542591239590.00799809679771-0.01854488855240.4525839560890.19079409513-0.6704390760370.09693754152440.37838533507-0.06502375295320.06573236820890.437274830628-0.1377854997110.5579189043140.75278113201435.1970952588.81405548877
131.57008022544-1.46036844847-0.8870053426833.192625063111.825916587142.52087688202-0.088762639654-0.0263534979436-0.06975504385990.452804869040.145138157865-0.1081169828780.5136680849450.2445133625-0.01852676599320.43860475642-0.0156283625359-0.006196805212530.390213286926-0.0644356894480.49963234761819.908282759813.61936668752.75043689223
145.85972249428-2.40782144637-0.1156654692455.493075618710.5169689177862.92443921925-0.188712238620.815821575285-0.472439137316-0.3368976373050.4117582007940.1925781523460.440209482458-0.266366145808-0.0399221035170.635867814362-0.1809535448080.05391937520240.900055691105-0.09918472181120.38189915739617.59189503925.03540803648-40.32334127
156.71846297553-3.2102552317-0.545935010696.641445988712.077837797484.7851999499-0.08474325100011.096410658610.576690241564-0.9348631037280.1506281655270.00444731223212-0.429499560863-0.4472693997570.03922190772560.735578261719-0.0862772808704-0.02405990918360.9628924940550.05358290159820.54071643342412.580718444218.1163899401-42.0552764836
162.10359644125-0.0830600681275-0.06952233207672.9147304222-0.1162757636162.89374825038-0.2628522809640.878796200234-0.266127075433-0.8742967333890.352253850183-0.429651545810.5054161386380.269897515884-0.03536826938680.791750165288-0.1326049904110.1714116015350.910500527015-0.2388395022190.58773521804127.6529977110.558069322816-40.958348012
172.25841727895-0.0802521896412-0.1200038280652.565722847510.05249454276762.88825390159-0.1250867037010.699244653171-0.676922142049-0.4887259841570.1466973130470.1268726611230.785892854397-0.231368742402-0.01134850783990.87963715313-0.1446756248160.06165041586480.760140146728-0.2518038688870.62722520322215.2425466994-9.65390525054-33.9492745236
182.79050081983-1.143787189380.2811413558363.442211341240.07911819771553.298727753520.0401601640.356189405103-0.327588568425-0.39402837359-0.105257509010.3510371667630.423516949635-0.4824559614020.07183500372550.521336060482-0.08785772458180.006774411954950.597708402385-0.162724007670.43002909667710.59686272112.81495721851-24.8154613499
193.07300739775-1.08333946417-0.2754621418581.69626865026-0.03516103352622.99052470764-0.1582259373860.466538978563-0.473140908352-0.180591419876-0.005055385910740.2964756694480.629707405373-0.258470575940.153351835490.619343363221-0.1451419158640.04601592145860.569450521817-0.1565137716430.5213287434298.8080081954-3.86615545422-21.0556568487
204.658461234210.0250788592094-0.7384223663812.24705059746-2.039060151891.9039843392-0.2710707744210.284368276678-0.6539278819910.05629169635820.21750848637-0.1558945471471.004506962260.5187657603480.09563632813130.8782401538610.04991936074130.06199710592810.57127595079-0.2435736238530.73678565154330.1954348782-16.5044974776-24.0449513324
213.8787105119-2.168695574570.6192830330179.08703626281-0.118304700124.44095313549-0.264808109371-0.2923566730.3610305342550.8811019993830.000960422856734-0.612862702602-0.1599861412710.274829703926-0.01548855080670.929889256944-0.1556804324630.05065000803950.787961128924-0.2709238376330.84344959641324.859657239799.717997252482.0897559141
222.32127426293-2.241019884330.7247287959566.366941352361.306901868521.22921348342-0.0829113658849-0.389339744485-0.08593833511461.293399445260.36647467924-0.6220299830120.2401988979790.387565231654-0.3133542472231.18011267029-0.00269409453646-0.1867119352660.813594122696-0.2792705311120.83560840755731.587071840982.894459805182.1866291524
230.256900609395-0.634534128569-0.9557018261612.734696783433.053138178884.135427142860.076095111361-0.0495979393999-0.02951030340010.3250598947110.576220797152-0.7855545265670.4567578297490.714768640503-0.5637172247140.4790311986010.0886681041590.003687943278190.871490544987-0.2674977165630.83863584720942.737234621528.86195525515.068199454
242.809600250050.851245835539-1.793495655493.35901239086-0.2331121300126.6126280222-0.409214201690.391168163563-0.828021837694-0.1856920821620.109956004306-0.06570506716241.56087480853-0.5910568787340.3328338034230.936005821936-0.1079806944670.1100223722510.55300653238-0.130930238970.7060399196456.1989947543755.115725780169.8125053865
254.210627506374.12545068715-2.829880194339.29442308041-9.039012637429.375212406980.397086136211-0.3081562735830.1756519153280.841404453856-0.185777647992-0.701797598746-0.6214410955090.856011199221-0.2066741238350.6809849922960.0489768223707-0.03439564509660.782912017311-0.003236870306510.71052064715311.306527649866.170820423497.396526665
262.61160265887-0.111912401411-0.2923841396952.6847878212-1.282923269324.93841966801-0.208811028485-0.842949040214-0.5987041799940.609405339882-0.15514227972-0.6936180128610.6615065807071.177287696140.3075846283061.034333893710.211483356220.02080118944430.999236205090.2308255484820.98156237360811.791111962755.794215811103.512867979
271.58956083133-0.493921513472-1.456960887650.3132011858351.059525791843.34595877666-0.626305576073-0.0491078043589-1.276399294020.297450777026-0.156559153489-0.323373332380.7531113281490.4473690403110.8144681612362.005409465120.2924584046140.2840833789440.9113638705410.3080343971381.611684925454.8608330049539.4126526551104.201415692
282.818824191710.134471728147-2.812901218371.07328026605-0.01108426277645.38654547861-0.3505398116580.0182143374984-0.6256567930360.3182422857970.2817627511890.1363483437850.831350189978-0.3258619630840.02280207442730.8321694069930.01672126655140.07716317965660.4490236494740.06153258984170.695610703967-3.3616364971457.886919361491.0508599546
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 1 through 71 )AA1 - 711 - 71
22chain 'A' and (resid 72 through 259 )AA72 - 25972 - 259
33chain 'A' and (resid 260 through 306 )AA260 - 306260 - 306
44chain 'A' and (resid 307 through 336 )AA307 - 336307 - 336
55chain 'A' and (resid 337 through 438 )AA337 - 438337 - 438
66chain 'B' and (resid 1 through 88 )BF1 - 881 - 86
77chain 'B' and (resid 89 through 238 )BF89 - 23887 - 236
88chain 'B' and (resid 239 through 296 )BF239 - 296237 - 290
99chain 'B' and (resid 297 through 437 )BF297 - 437291 - 423
1010chain 'C' and (resid 1 through 223 )CK1 - 2231 - 223
1111chain 'C' and (resid 224 through 311 )CK224 - 311224 - 311
1212chain 'C' and (resid 312 through 372 )CK312 - 372312 - 372
1313chain 'C' and (resid 373 through 440 )CK373 - 440373 - 440
1414chain 'D' and (resid 1 through 27 )DO1 - 271 - 27
1515chain 'D' and (resid 28 through 59 )DO28 - 5928 - 57
1616chain 'D' and (resid 60 through 180 )DO60 - 18058 - 178
1717chain 'D' and (resid 181 through 238 )DO181 - 238179 - 236
1818chain 'D' and (resid 239 through 295 )DO239 - 295237 - 287
1919chain 'D' and (resid 296 through 401 )DO296 - 401288 - 385
2020chain 'D' and (resid 402 through 441 )DO402 - 441386 - 425
2121chain 'E' and (resid 6 through 20 )ES6 - 201 - 15
2222chain 'E' and (resid 21 through 46 )ES21 - 4616 - 26
2323chain 'E' and (resid 47 through 141 )ES47 - 14127 - 121
2424chain 'F' and (resid 1 through 66 )FT1 - 661 - 66
2525chain 'F' and (resid 67 through 96 )FT67 - 9667 - 96
2626chain 'F' and (resid 97 through 222 )FT97 - 22297 - 197
2727chain 'F' and (resid 223 through 257 )FT223 - 257198 - 229
2828chain 'F' and (resid 258 through 380 )FT258 - 380230 - 342

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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