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- PDB-8sso: AurA bound to danusertib and inhibiting monobody Mb2 -

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基本情報

登録情報
データベース: PDB / ID: 8sso
タイトルAurA bound to danusertib and inhibiting monobody Mb2
要素
  • Aurora kinase A
  • Mb2
キーワードTRANSFERASE / Complex / Kinase / Monobody
機能・相同性
機能・相同性情報


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / germinal vesicle / meiotic spindle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / negative regulation of protein binding / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / molecular function activator activity / AURKA Activation by TPX2 / regulation of cytokinesis / liver regeneration / regulation of signal transduction by p53 class mediator / mitotic spindle organization / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / kinetochore / response to wounding / spindle / spindle pole / G2/M transition of mitotic cell cycle / mitotic spindle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / microtubule cytoskeleton / midbody / protein autophosphorylation / basolateral plasma membrane / Regulation of TP53 Activity through Phosphorylation / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / eukaryotic translation initiation factor 2alpha kinase activity / 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 / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / ciliary basal body / protein phosphorylation / protein heterodimerization activity / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / nucleus / cytosol
類似検索 - 分子機能
Aurora kinase A / Aurora 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
Chem-627 / ACETATE ION / Aurora kinase A
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.97 Å
データ登録者Ludewig, H. / Kim, C. / Kern, D.
資金援助 米国, 1件
組織認可番号国
Howard Hughes Medical Institute (HHMI) 米国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2023
タイトル: A biophysical framework for double-drugging kinases.
著者: Kim, C. / Ludewig, H. / Hadzipasic, A. / Kutter, S. / Nguyen, V. / Kern, D.
履歴
登録2023年5月8日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年9月6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: Aurora kinase A
B: Mb2
D: Aurora kinase A
E: Mb2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)86,8199
ポリマ－85,6894
非ポリマー1,1295
水9,656536
1
A: Aurora kinase A
B: Mb2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,4996
ポリマ－42,8452
非ポリマー6554
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-9 kcal/mol
Surface area17330 Å2
手法PISA
2
D: Aurora kinase A
E: Mb2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)43,3193
ポリマ－42,8452
非ポリマー4751
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-10 kcal/mol
Surface area16780 Å2
手法PISA
単位格子
Length a, b, c (Å)65.619, 73.225, 179.315
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 , 2種, 4分子 ADBE

#1: タンパク質 Aurora kinase A / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / Breast tumor-amplified ...Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / Breast tumor-amplified kinase / Ipl1- and aurora-related kinase 1 / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase Ayk1 / Serine/threonine-protein kinase aurora-A


分子量: 32990.754 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: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: O14965, non-specific serine/threonine protein kinase
#2: タンパク質 Mb2


分子量: 9853.987 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)

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非ポリマー , 4種, 541分子

#3: 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
#4: 化合物 ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C2H3O2
#5: 化合物 ChemComp-627 / N-[(3E)-5-[(2R)-2-METHOXY-2-PHENYLACETYL]PYRROLO[3,4-C]PYRAZOL-3(5H)-YLIDENE]-4-(4-METHYLPIPERAZIN-1-YL)BENZAMIDE / Danusertib / PHA-739358 / ダヌセルチブ


分子量: 474.555 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C26H30N6O3 / タイプ: SUBJECT OF INVESTIGATION
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 536 / 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: 2.52 Å3/Da / 溶媒含有率: 51.09 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.5
詳細: Crystals of AurA in complex with Mb2 and danusertib were obtained by combining 0.5 ul of 300 uM (10 mg/mL) AurA + 315 uM (4 mg/mL) Mb2 + 1 mM danusertib with 0.5 ul of 0.1 M BIS-TRIS pH 5.5 + ...詳細: Crystals of AurA in complex with Mb2 and danusertib were obtained by combining 0.5 ul of 300 uM (10 mg/mL) AurA + 315 uM (4 mg/mL) Mb2 + 1 mM danusertib with 0.5 ul of 0.1 M BIS-TRIS pH 5.5 + 0.2 M Ammonium acetate + 25 percent PEG3350. Crystals were grown at 18 degC by sitting drop. Crystals were harvested and subsequently flash frozen

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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: ALS / ビームライン: 5.0.1 / 波長: 0.97741 Å
検出器タイプ: DECTRIS PILATUS3 2M / 検出器: PIXEL / 日付: 2020年12月18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: 0.97741 Å / 相対比: 1
反射解像度: 1.97→44.19 Å / Num. obs: 59706 / % possible obs: 95.64 % / 冗長度: 9.3 % / Biso Wilson estimate: 31.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0803 / Net I/σ(I): 20.24
反射 シェル解像度: 1.97→2.044 Å / Rmerge(I) obs: 1.118 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 6010 / CC1/2: 0.731

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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
Aimless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: 1.97→44.19 Å / SU ML: 0.2295 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 25.4504
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2343 2918 4.96 %
Rwork0.1917 55890 -
obs0.1938 58808 95.48 %
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: 49.21 Å2
精密化ステップサイクル: LAST / 解像度: 1.97→44.19 Å
タンパク質核酸リガンド溶媒全体
原子数5536 0 82 536 6154
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00275843
X-RAY DIFFRACTIONf_angle_d0.56437945
X-RAY DIFFRACTIONf_chiral_restr0.0439869
X-RAY DIFFRACTIONf_plane_restr0.00481002
X-RAY DIFFRACTIONf_dihedral_angle_d5.7894808
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.010.33441560.29312661X-RAY DIFFRACTION98.26
2.01-2.040.30841330.26792769X-RAY DIFFRACTION100
2.04-2.080.33131410.29562742X-RAY DIFFRACTION99.97
2.08-2.120.32111430.24942755X-RAY DIFFRACTION99.97
2.12-2.160.3061500.23472749X-RAY DIFFRACTION100
2.16-2.210.29211360.23452757X-RAY DIFFRACTION100
2.21-2.260.4717610.3961065X-RAY DIFFRACTION39.04
2.26-2.320.29461220.27162235X-RAY DIFFRACTION81.16
2.32-2.380.22221430.19662763X-RAY DIFFRACTION99.97
2.38-2.450.24791430.2012778X-RAY DIFFRACTION100
2.45-2.530.24711240.19512797X-RAY DIFFRACTION100
2.53-2.620.2631520.19342755X-RAY DIFFRACTION99.97
2.62-2.720.20681370.18452787X-RAY DIFFRACTION99.97
2.72-2.850.24471460.19082775X-RAY DIFFRACTION100
2.85-30.20731270.19272808X-RAY DIFFRACTION100
3-3.180.2491430.19512785X-RAY DIFFRACTION100
3.18-3.430.24591400.19582799X-RAY DIFFRACTION99.97
3.43-3.780.23781330.18452469X-RAY DIFFRACTION87.52
3.78-4.320.23441700.16592801X-RAY DIFFRACTION99.5
4.32-5.440.18931470.14872874X-RAY DIFFRACTION99.97
5.44-44.190.17091710.16862966X-RAY DIFFRACTION99.18
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)
12.223138699270.136067789169-0.48519114321.60264525312-1.019616323751.46574559630.0521246640675-0.356713408597-0.2477991825350.1502039717450.06687282711480.1167076402640.228231492736-0.448089173236-0.0398333926910.330118301904-0.07933239020650.0194810270840.6958962111340.007159810568050.2919290304635.6862166231615.588050269527.5743373845
21.30790990791-0.1121675380070.250178565040.54438506421-0.1974460268362.470181036580.0502857297047-0.154595825525-0.0264525359490.06779017867640.01321409692140.04812021997790.207266660537-0.399169399534-0.04032953057290.1744780486120.004854996182880.01213597810260.3123212247620.0003372058447180.21580525251112.43647073519.929068934614.1702492321
32.90205715106-0.2224534039950.4243306524621.80297316145-0.2078457625362.95485475397-0.002071362843430.146057349880.02774675051360.0137692845988-0.0158683129121-0.0358374597510.08351166805260.1391423907340.01073284982890.118349906418-0.0113121738470.02287860307470.204502373478-0.007105567396980.16510687046726.900284760719.44402226824.6766662606
46.63301134488-1.11464746119-1.182251267515.577198183292.106218271518.566716256690.6465225620110.9689636366980.27754022129-0.9149678791960.3688210906810.847561733105-0.321279300297-0.443521170847-0.7857006446440.515647214721-0.167366397861-0.03344549085930.9623402593390.243817660430.473302822198-3.08949591844.5321983187144.9299776906
55.136501984881.61529851407-0.6109461874417.62849304354-0.2379722968770.07289942010890.278643110126-0.782761916236-0.1977493747170.1251366891610.06999054019950.3814235878140.739934011218-0.378689791125-0.222066625590.386375122375-0.07421931997230.03135563432730.6526607984810.1733445633560.419224289467-3.76634269624-4.9036794772860.3991058962
64.11778414892.32009988517-3.537647992414.02810737904-5.423904842517.34365421460.02627172184190.156849911840.2732212599680.101618528425-0.0254182118151-0.01307067292710.132830645380.0718184702725-0.006351901824670.307305499645-0.1116586556910.03464962528740.5785584929460.08069994911070.343381549093.739455356661.1251548948253.7354152085
71.71427471358-2.51625994089-2.536630599314.154309389744.551055295155.237289014160.305774938469-2.278691641842.604699381170.4812821001180.03026100201170.739531522883-2.1684532608-0.0462543061977-0.1749793204061.423997800420.03048324477660.491014471630.85751980039-0.2336450866271.01150744383-0.78472200143915.073819073265.0264540657
84.588701695421.95249165899-3.049630146768.7652743026-2.584058080632.707455267760.643012739842-0.4315153467430.8194420083810.406504507122-0.613482694777-0.339017175941-0.9919530020681.467404685590.01315979602260.444967021612-0.2063933932920.02810611846770.7303643894450.03576843119650.4401286598269.446572240944.7340229279456.9466063418
92.895666290651.02104329848-1.171510672554.95387787279-2.594211276779.721743311760.238113733207-0.116947084753-0.2074837419690.2534490375150.0828768235315-0.5590227540240.1493450094410.0571041012269-0.2248436549550.281514754111-0.120024050106-0.01166990292340.5705404736280.01447427309540.4097155338292.97768537166-0.22985732016861.667357159
103.928348918342.14183815406-0.4307849510463.14734026713-1.420284652165.337411592010.217899626167-0.09286205712550.8332384052950.08780002622190.3284664699460.761048022676-0.391439517612-0.303162581501-0.5973277248250.3338760402290.02003721737220.1266604638270.5350710526940.05628123741960.448353763151-0.407446352147.1822906981156.8726758168
114.544082432962.72285359477-2.273291980143.10148087356-2.923355479687.048465066240.1952246409890.07185119235210.4729501017570.05478933193960.3489068071390.545299597865-0.264423625157-0.0436994646004-0.4771796835390.283846524967-0.03924175293140.01831290001970.6542421996220.1042331306760.4148584299852.793579864616.4278264044248.9346705194
122.90097760312-1.47270196920.3866765481481.619974844521.374180442862.955507349650.039476333050.0684648635106-1.013911307380.369366869359-0.07070518493140.5493482083031.14963246208-0.1061562587910.1482051240661.42758567583-0.06360754442640.1188529270180.429143108336-0.1339216656430.5798749310630.0567107092-17.856499783918.9206871605
132.212724339850.5177760014621.05508363563.05682599171-0.08717908445471.560652484660.206068290925-0.19352450388-0.137565867073-0.121390614033-0.006753347549060.1439040378080.694344679496-0.2500706296-0.1467985290280.7962166128830.00649277427930.06748956384160.3580104946010.04371578848370.33429328153832.1216630323-10.156581703318.3989306149
141.86859989243-0.520696071293-0.2228191073282.46467936635-0.7040368786844.020701868080.013209403035-0.167815597668-0.2849960868420.0510517200768-0.1552354885920.09131900566690.7137852925440.18426582760.1185532341690.3707663221250.0152853668795-0.006943986695950.4356966889590.04200037801250.3165233079537.0060045232.4034999036533.6043614786
152.92148402112-0.6349756414720.9099911515122.82002646694-1.029636692094.563543091930.139838726013-0.3586692906780.2278734009260.365485281962-0.269858478441-0.210152889197-0.137984751440.3165914779320.1723086609290.34928559124-0.077311698923-0.0601107573430.495955776165-0.01620083184530.27020197592138.507737472811.179808034142.0995639241
162.546577745792.5019571733-0.4349805273197.935841489611.802593108172.671921869440.0687647813999-0.0445887905447-0.2830929040810.4323291578620.0136944917276-0.1388416522040.3904755401420.00213255026687-0.04721188976331.23037305668-0.161308727553-0.3679234182180.272765542119-0.1944737630971.068043898918.7570558644-20.08836973191.94036013923
176.713244738262.238542504543.025895073097.244175880083.907782332345.01779564774-0.1181720429850.832750663210.163050498691-1.086203151720.911967538711-0.09074941241.062076745820.624923114559-0.7952235670171.00255033262-0.224069497589-0.06012795107140.542431749062-0.2108388974320.6726280675615.7320987037-20.8114380066-13.9526801793
183.80791806051-1.193398104722.064291284692.243259166490.08914738553391.40784606093-1.117154002190.355490681783-0.727490127373-0.5735464814190.4553210076410.1583140257981.16022296075-0.7803437329620.3331176937690.956416721911-0.2268106507010.1776191136740.5021810356420.002684202171680.53510737586714.6477927384-11.49413046222.79402863564
191.605981014641.014099920911.098635733014.00548008612-1.144662290259.77220827201-0.187508926050.876544281738-0.508178239373-0.7527735158710.412581677202-0.7212390018180.9631722587891.24560568519-0.3376076404470.72710510105-0.1407464768710.009859022144020.629588489427-0.3127174214340.71631584850124.6166636915-14.2861943267-9.58885365801
204.19639803644-4.41330329594-1.344924517146.879606069393.902490432493.158712720480.3611835114121.25244722346-0.179421998696-1.148085625880.0998937366896-0.8294403287230.1383672763270.88336073899-0.6683380710971.03673267177-0.10440278426-0.03983051029510.823663604514-0.03714426452660.6204848961427.3503684551-13.7013740088-12.1891107239
212.75332070385-3.85075446678-1.428753568695.527733624172.906718951825.629480685240.1070166986710.759230039151-0.907914587303-1.448819474010.355295170567-0.6720387147450.5990009406610.615552092434-0.4549473301090.982796364461-0.2587567721550.05413272929290.497422870667-0.4132737513140.94105678278419.8000273311-17.5908413228-15.4805023823
224.65798644098-1.61699703282-0.3805020650612.41090021378-1.834513111352.116916013370.2581408655220.837703597523-0.384961889924-1.328866906420.218034942692-1.235277617390.511987993241.03518975439-0.4160729944310.8116925571170.0660711339670.09440489079310.640456549632-0.3567509829710.87988215475524.9607526977-17.1083617144-7.08680468432
230.560757119115-0.301655851964-0.4035634089312.61492675765-0.7293184955350.6664633052520.3092721266450.0163245721813-0.733098506720.768145730685-0.0351216407173-0.01744018389580.1342493945310.1340660639490.1283442668960.716041059839-0.09747327917-0.06748093878810.242226475817-0.1152226862950.49962929804824.1630106642-8.434356199155.78401548464
240.43699879661.127437215410.5472530537365.996856206840.123463021241.872809654310.1414058198310.19769642346-0.341684403045-0.2224499019250.0368694176168-0.9216656580280.8315301994440.189598744756-0.689744315581.0428857290.0385235639816-0.1881626316350.477335544215-0.5616152009121.07601161123.1109713367-25.9996934128-10.9763194258
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 127 through 201 )AA127 - 2011 - 75
22chain 'A' and (resid 202 through 291 )AA202 - 29176 - 158
33chain 'A' and (resid 292 through 389 )AA292 - 389159 - 256
44chain 'B' and (resid 2 through 10 )BD2 - 101 - 9
55chain 'B' and (resid 11 through 16 )BD11 - 1610 - 15
66chain 'B' and (resid 17 through 40 )BD17 - 4016 - 39
77chain 'B' and (resid 41 through 47 )BD41 - 4740 - 46
88chain 'B' and (resid 48 through 53 )BD48 - 5347 - 52
99chain 'B' and (resid 54 through 68 )BD54 - 6853 - 67
1010chain 'B' and (resid 69 through 76 )BD69 - 7668 - 75
1111chain 'B' and (resid 77 through 93 )BD77 - 9376 - 92
1212chain 'D' and (resid 127 through 145 )DF127 - 1451 - 19
1313chain 'D' and (resid 146 through 217 )DF146 - 21720 - 91
1414chain 'D' and (resid 218 through 324 )DF218 - 32492 - 187
1515chain 'D' and (resid 325 through 389 )DF325 - 389188 - 252
1616chain 'E' and (resid 4 through 9 )EG4 - 91 - 6
1717chain 'E' and (resid 10 through 24 )EG10 - 247 - 21
1818chain 'E' and (resid 25 through 32 )EG25 - 3222 - 29
1919chain 'E' and (resid 33 through 40 )EG33 - 4030 - 37
2020chain 'E' and (resid 41 through 53 )EG41 - 5338 - 47
2121chain 'E' and (resid 54 through 69 )EG54 - 6948 - 63
2222chain 'E' and (resid 70 through 77 )EG70 - 7764 - 71
2323chain 'E' and (resid 78 through 86 )EG78 - 8672 - 80
2424chain 'E' and (resid 87 through 92 )EG87 - 9281 - 86

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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