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- PDB-9ks5: The crystal structure of ABL1 in complex with K-CNBA-1 -

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基本情報

登録情報
データベース: PDB / ID: 9ks5
タイトルThe crystal structure of ABL1 in complex with K-CNBA-1
要素Tyrosine-protein kinase ABL1
キーワードUNKNOWN FUNCTION / ABL1 / K-CBA-1 / LYSINE MODIFICATION / IRREVERSIBLE COVALENT PROBE
機能・相同性
機能・相同性情報


: / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process ...: / positive regulation of actin filament binding / negative regulation of ubiquitin-protein transferase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / activation of protein kinase C activity / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / delta-catenin binding / Role of ABL in ROBO-SLIT signaling / transitional one stage B cell differentiation / regulation of postsynaptic specialization assembly / regulation of modification of synaptic structure / nicotinate-nucleotide adenylyltransferase activity / cerebellum morphogenesis / neuroepithelial cell differentiation / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / microspike assembly / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / bubble DNA binding / mitochondrial depolarization / regulation of cell motility / positive regulation of establishment of T cell polarity / activated T cell proliferation / cellular response to dopamine / positive regulation of blood vessel branching / proline-rich region binding / negative regulation of mitotic cell cycle / regulation of Cdc42 protein signal transduction / mitogen-activated protein kinase binding / regulation of hematopoietic stem cell differentiation / syntaxin binding / positive regulation of dendrite development / alpha-beta T cell differentiation / positive regulation of cell migration involved in sprouting angiogenesis / peptidyl-tyrosine autophosphorylation / regulation of axon extension / regulation of T cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of cell-cell adhesion / neuromuscular process controlling balance / HDR through Single Strand Annealing (SSA) / Myogenesis / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor-beta signaling pathway / RUNX2 regulates osteoblast differentiation / positive regulation of vasoconstriction / Fc-gamma receptor signaling pathway involved in phagocytosis / vascular endothelial cell response to oscillatory fluid shear stress / regulation of endocytosis / Bergmann glial cell differentiation / regulation of microtubule polymerization / negative regulation of long-term synaptic potentiation / myoblast proliferation / associative learning / negative regulation of cellular senescence / actin monomer binding / signal transduction in response to DNA damage / positive regulation of focal adhesion assembly / canonical NF-kappaB signal transduction / negative regulation of BMP signaling pathway / RHO GTPases Activate WASPs and WAVEs / ephrin receptor signaling pathway / cardiac muscle cell proliferation / positive regulation of T cell migration / BMP signaling pathway / cellular response to transforming growth factor beta stimulus / endothelial cell migration / negative regulation of endothelial cell apoptotic process / negative regulation of double-strand break repair via homologous recombination / regulation of cell adhesion / mismatch repair / ephrin receptor binding / spleen development / four-way junction DNA binding / positive regulation of stress fiber assembly / ruffle / ERK1 and ERK2 cascade / phosphotyrosine residue binding / actin filament polymerization / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / positive regulation of interleukin-2 production / substrate adhesion-dependent cell spreading / positive regulation of mitotic cell cycle / SH2 domain binding / protein kinase C binding / peptidyl-tyrosine phosphorylation / response to endoplasmic reticulum stress / thymus development / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of release of sequestered calcium ion into cytosol / integrin-mediated signaling pathway / post-embryonic development
類似検索 - 分子機能
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Tyrosine-protein kinase ABL1
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: 2.2 Å
データ登録者Zhang, Z.M. / Duan, L.P.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: To Be Published
タイトル: O-Cyanobenzaldehydes (CNBA) Irreversibly Modify both Buried and Exposed Lysine Residues in Live Cells
著者: Zhang, Z.M. / Duan, L.P.
履歴
登録2024年11月29日登録サイト: PDBJ / 処理サイト: PDBC
改定 1.02025年12月3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: Tyrosine-protein kinase ABL1
B: Tyrosine-protein kinase ABL1


分子量 (理論値)分子数
合計 (水以外)64,2672
ポリマ－64,2672
非ポリマー00
水6,774376
1
A: Tyrosine-protein kinase ABL1


分子量 (理論値)分子数
合計 (水以外)32,1341
ポリマ－32,1341
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase ABL1


分子量 (理論値)分子数
合計 (水以外)32,1341
ポリマ－32,1341
非ポリマー00
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)106.48, 134.99, 58.0
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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要素

#1: タンパク質 Tyrosine-protein kinase ABL1 / Abelson murine leukemia viral oncogene homolog 1 / Abelson tyrosine-protein kinase 1 / Proto- ...Abelson murine leukemia viral oncogene homolog 1 / Abelson tyrosine-protein kinase 1 / Proto-oncogene c-Abl / p150


分子量: 32133.697 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: ABL1, ABL, JTK7 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P00519, non-specific protein-tyrosine kinase
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 376 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY
Has protein modificationY

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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: 3.29 Å3/Da / 溶媒含有率: 62.65 %
結晶化温度: 298.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5
詳細: 0.1 M Sodium citrate, 2% Tacinate (pH 5.0) and 16% w/v PEG 3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: CAMD / ビームライン: GCPCC / 波長: 0.978 Å
検出器タイプ: DECTRIS PILATUS 300K / 検出器: PIXEL / 日付: 2024年9月15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: 0.978 Å / 相対比: 1
反射解像度: 2.2→32.2 Å / Num. obs: 43305 / % possible obs: 100 % / 冗長度: 9.8 % / Biso Wilson estimate: 8.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.048 / Rrim(I) all: 0.156 / Net I/σ(I): 15
反射 シェル解像度: 2.2→2.27 Å / Num. unique obs: 3714 / CC1/2: 0.836

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692+SVN精密化
HKL-3000データ削減
HKL-3000データスケーリング
Cootモデル構築
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.2→32.17 Å / SU ML: 0.226367327838 / 交差検証法: FREE R-VALUE / σ(F): 1.34351548402 / 位相誤差: 20.6713067915
Rfactor反射数%反射
Rfree0.211556250836 1555 3.59579142097 %
Rwork0.170247344589 41690 -
obs0.171712121203 43245 99.9468429324 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 39.1266114246 Å2
精密化ステップサイクル: LAST / 解像度: 2.2→32.17 Å
タンパク質核酸リガンド溶媒全体
原子数4321 0 76 376 4773
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006346795291974517
X-RAY DIFFRACTIONf_angle_d0.8803048784626117
X-RAY DIFFRACTIONf_chiral_restr0.033813202477646
X-RAY DIFFRACTIONf_plane_restr0.00335285590363762
X-RAY DIFFRACTIONf_dihedral_angle_d13.63683908041657
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2710.3219585196381390.2191374230523734X-RAY DIFFRACTION100
2.271-2.35220.262985249871390.2072667089673737X-RAY DIFFRACTION99.974206861
2.3522-2.44630.2274129331811400.1955227496323738X-RAY DIFFRACTION100
2.4463-2.55760.2605300595461390.1907110672453743X-RAY DIFFRACTION99.9742467165
2.5576-2.69240.2519603159271400.1960288656673749X-RAY DIFFRACTION99.9742930591
2.6924-2.8610.2328277352891400.194041256623752X-RAY DIFFRACTION99.9486389317
2.861-3.08170.2458562425731410.1882176158093784X-RAY DIFFRACTION99.9745287825
3.0817-3.39150.2258542752021410.1798976463853778X-RAY DIFFRACTION99.9489926039
3.3915-3.88160.2011345191420.1513825668223817X-RAY DIFFRACTION99.9747474747
3.8816-4.88760.1707343609991450.1318716804213851X-RAY DIFFRACTION99.9499749875
4.8876-32.170.1640080787891490.1595202545474007X-RAY DIFFRACTION99.7360211183
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)
13.010789689473.289095204313.947879283644.861305835956.04798688377.55789026035-0.201167300311-0.8437135351760.708639779290.604931240287-0.5255676895880.36836782688-0.153321854639-1.793835947060.7269160377150.4512023736060.108589740941-0.07336397556430.623531018406-0.1120484447570.364126312351-29.385500547221.13463142737.88134342064
22.87656431062-3.661273183730.2960038532969.290323080132.502849620155.5282462977-0.4329814971891.326159686620.0766380708735-0.030473250217-0.21756322329-0.518499132487-0.128494262934-0.1959936526490.6778658994760.241903538494-0.01784437119080.01137955508080.4047530701530.03152542500810.227941711466-12.708898945419.0806716635.53145020181
35.00711587587-2.941798495254.325383188734.53513993785-0.8160131894076.18922258624-0.249791045220.09936224094490.6609593664140.141946129634-0.31443128564-0.212062502613-0.4591832504870.1276565666190.5071584622210.2271194446120.01136438444710.02947853048250.249494825451-0.02353754229320.270063291013-22.353558567422.0682549788-0.64312130592
42.37932602383-0.9120859510710.2268006444231.46410556192-0.03501517543041.89196259769-0.152091437346-0.1311865362780.1089148884420.2103925566740.0761492528420.120811088134-0.114975828387-0.2377196960380.05628806876670.1708802232840.01442273782270.01714618727430.165733660365-0.004687983171610.166750384996-20.80242328319.84614542914-10.3710347734
54.51818477443-2.823512194020.5294286059934.55194927722-0.8603056543241.946576346550.07105691702980.1065802707460.388971118982-0.0917648722248-0.118225764629-0.160075315808-0.206037044572-0.1639600819930.05293719214320.1823839823970.02720425470590.0178037554760.1872033656430.009945299421880.12729903707-19.411026936717.1152612684-26.1304307877
63.171265355040.8120456827940.4759228187045.28851081196-5.996136211138.37680237014-0.1618360852110.12657458279-0.01974036882740.219010856352-0.100359531091-0.289741911625-0.3651711641830.4320289048720.3203474965910.1314076315540.04916245167110.01334598822910.2372676904640.003255300572420.188637563027-5.3751764762311.0404393656-25.9377727915
74.903334265984.842002759046.464207006894.89522145416.465418657968.58695588271-0.2380761858230.4794127092010.748701520021-0.691890796723-0.027554751020.104668607108-0.86238053267-0.1262090472840.1937737716330.3186319503330.04015173559880.01760282137550.2808925876550.06835434303130.236003108401-11.690388567719.8521108366-36.4813730977
83.4335897322-2.116870746561.825892374773.33258951335-4.566506924517.595416491070.05038238902590.117745279034-0.11815427482-0.367736319442-0.332136789244-0.5832362234060.5864772197850.4526769186770.2440136543830.2734544521340.06195430689070.001845666362120.257972437985-0.01773876188080.201843623335-9.774291175764.53206147593-32.984341083
99.52391943575-4.215907335465.286151026664.66637682228-5.710863838317.10222341003-0.11960544703-0.0556353117262-0.328809145725-0.4365173603480.4745466607290.02002175401870.4737276871230.125467278512-0.2560019998660.243452798821-0.003474976189150.03746850588850.273092997835-0.07667589859780.179355337073-17.00144289610.377763332476-30.9020912022
107.934150708781.66124613668-2.133078338664.9132951414-1.224944955073.355265319860.1740352466180.740090709372-0.0779231287241-0.576102182138-0.05646263447890.2932080141580.284380732943-0.601402960755-0.1358877347780.2139990021010.0327757024597-0.01299267130070.363379850246-0.04947454662870.149253116385-24.58366866859.78772609055-33.7398835868
116.35815697552-4.768777748563.029315650773.56485028912-2.403642534227.852578521170.1016773193640.108431228988-0.986958442444-0.03643742365070.09599809959920.5713976743161.20145025636-0.627404583061-0.2445872953590.311074253691-0.1092569693850.03771239059750.274384812168-0.03257583317750.337859755769-24.3640445247-4.69147918396-21.0505109014
124.053763892250.549278756888-2.827026011783.27305280083-0.6713471811357.9938426401-0.1999202004970.5484474023070.450129056049-0.3023438474680.329094243244-1.7382660181-1.079612435381.71225131025-0.09947510159720.572239886739-0.2817571630330.01843186388760.8253342159770.000418374415181.09296878847-9.7955052130357.1793689809-11.3179907863
133.347488792650.41526017715-0.6794534385033.851795553072.188988305857.074862646870.05621067080090.631875767657-0.12288242341-0.278551060951-0.238997384167-1.33309484433-0.4233192537530.7470225090850.09414652982860.423023891944-0.1254908979580.09456499367040.768460849109-0.10419588820.819262262882-14.69655487255.8234608918-16.4391431763
143.703567668450.0936877009405-3.746062329493.606155960093.736312961297.905522936840.6280422916410.3786254238770.217962851966-0.784207914626-0.175226121524-0.508129660366-1.27472908088-0.145169977501-0.4558813888820.4567443296540.02966410330770.1228798541530.4440549808380.03978510802690.546646700569-18.775005075362.7165020088-13.0258735345
154.134363706874.23897351055-6.089945845664.50535000036-6.329570033929.058367369760.5617985500690.3737970701211.256727968480.584688743828-0.1902017083010.919157368519-0.533693205739-0.695999349306-0.4277442326950.359215407354-0.0065348801035-0.03465212505160.405341313858-0.0636281893860.596159108334-23.737147155761.3407240555-3.32648494538
166.31368126324.9339083341-0.5952446227238.1857932308-0.5483998924526.19151976160.385608725605-0.2707389649040.1821896466140.334650517506-0.117372465671-0.86559780144-0.7828519591520.579577397016-0.2389287280070.3231650892090.0229494663932-0.07150831232910.339277193007-0.08075319686440.604818993083-18.876027944353.4637406871-5.1789317673
174.522941252812.600384493053.589177603647.972562031476.5873441186.3560579375-0.08591040710410.444132499332-0.210642456848-0.6776777771050.716193617679-1.13066347503-0.6109067424690.877712069053-0.7579743237240.28544870902-0.01592543383920.1367846527270.457834142051-0.02488323131070.509488946911-19.348709406751.1242846771-14.8995909437
189.65845856461-1.714013284521.563897881375.240184250772.551557637596.926796999360.1243273273630.8955981790240.0769056138691-1.41191047844-0.0230991556191-0.697893809571-0.1624732467890.385077434303-0.1531073455550.3008486159070.07146051771670.05582253699320.3940633156310.03976385511410.244188083593-32.559499410738.9274395172-25.815764688
194.084284040040.3208113748160.4670453531176.995222552685.469308041614.278632281-0.109813196046-0.165912758475-0.05322419055430.3031656084050.28085704597-0.3070010521780.2613925390930.372968867717-0.1634634767260.2398965658730.0687869125892-0.03512121732740.1856962276120.01323561825980.218122901059-34.229189532939.3381158284-8.1001200583
202.65483130371-2.97216503555-2.606955296488.596478900716.211203882724.594061462090.10292885636-0.1035832560230.280086002895-0.2132097451790.203542982094-0.467487011368-0.1001056903970.531945137195-0.3913835209730.2238920290730.0267143948841-0.007763436620940.259159014165-0.01282410478620.30115469819-31.814447317850.2037307409-7.20587324347
213.48917900313-4.70748481378-2.74973055046.613045651763.811269355032.20163673623-0.5504959760660.7825888715740.803369960781-1.03579826377-0.100326399711-0.549940842446-3.03079253860.5363162467130.632296801841.02426578768-0.128994463034-0.1587104971390.4044997381570.08031898041890.459846407965-40.555197731664.6735450336-8.83014343664
224.41618724417-4.83215091263-5.443196265327.607819087195.454292720236.80475064067-0.03253893960810.1942361704430.502222262027-0.5238260090380.0972593121144-0.0131753593833-0.4924529284260.167666996329-0.06827714743520.243675967968-0.0202735716581-0.03951087420190.1959531430270.02185938890410.250349878406-44.89282123254.94847413-15.5746075436
238.1755686999-0.3691475958226.081801259887.991867654351.880482010837.95636059167-0.567079883385-0.6720871830590.8810895203430.5184139808110.2482763083730.0707602166828-0.911252027992-0.2084136170460.2447844371960.4022138012970.0811440626351-0.02800574389350.276595081013-0.09076150108070.292559586836-47.279720771859.2582651307-5.36933667225
242.508843533760.428947740462-0.3896460275963.394408316252.405934478414.374386349830.08185453628630.3255332378910.142438831475-0.1640655992790.0973095657915-0.2560839072660.134467193570.0521733848734-0.1324994448440.1570672035080.07558423976090.003644201972450.204950118280.01743263764430.188980798671-43.974206010147.2883500234-17.0953575592
257.13962278358-3.66894987368-0.9623213480947.12229069950.655203328913.01624696890.09324987314050.4077998025270.0295770655982-0.430494044985-0.1997769331560.02895858023720.1404469085870.06932132700690.08123301957270.2021627812830.0267025009768-0.02818544048860.2099615342870.002295719577680.10153333562-53.760225845248.786312577-18.3384426057
268.32284564728-6.53398821714-5.706640322095.147317609614.487365641213.93673005583-0.07285494552040.137956705174-0.8310838631630.0277450956233-0.1287378815270.4118326288580.531138886093-0.4585741083820.07735661039810.289680735180.0257611832875-0.05289382847560.2511126728520.005069797922820.244847499161-49.57800009537.7724602444-12.6630086932
276.77413120639-5.76569215499-2.139230276076.776862691991.736827835511.91127248073-0.330003802011-0.218758758619-0.1666562983830.3944441719460.166483912130.02168013776560.1405974995570.0860084434120.1758449167990.2052582902570.0279933896967-0.01180659691170.1787608379550.02650626165640.146137941791-44.2606726438.5547004675-5.78516100365
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 233 through 241 )
2X-RAY DIFFRACTION2chain 'A' and (resid 242 through 250 )
3X-RAY DIFFRACTION3chain 'A' and (resid 252 through 292 )
4X-RAY DIFFRACTION4chain 'A' and (resid 293 through 392 )
5X-RAY DIFFRACTION5chain 'A' and (resid 394 through 433 )
6X-RAY DIFFRACTION6chain 'A' and (resid 434 through 444 )
7X-RAY DIFFRACTION7chain 'A' and (resid 445 through 453 )
8X-RAY DIFFRACTION8chain 'A' and (resid 454 through 465 )
9X-RAY DIFFRACTION9chain 'A' and (resid 466 through 475 )
10X-RAY DIFFRACTION10chain 'A' and (resid 476 through 485 )
11X-RAY DIFFRACTION11chain 'A' and (resid 486 through 500 )
12X-RAY DIFFRACTION12chain 'B' and (resid 233 through 247 )
13X-RAY DIFFRACTION13chain 'B' and (resid 248 through 265 )
14X-RAY DIFFRACTION14chain 'B' and (resid 266 through 279 )
15X-RAY DIFFRACTION15chain 'B' and (resid 280 through 291 )
16X-RAY DIFFRACTION16chain 'B' and (resid 292 through 310 )
17X-RAY DIFFRACTION17chain 'B' and (resid 311 through 322 )
18X-RAY DIFFRACTION18chain 'B' and (resid 323 through 336 )
19X-RAY DIFFRACTION19chain 'B' and (resid 337 through 356 )
20X-RAY DIFFRACTION20chain 'B' and (resid 357 through 392 )
21X-RAY DIFFRACTION21chain 'B' and (resid 394 through 402 )
22X-RAY DIFFRACTION22chain 'B' and (resid 403 through 407 )
23X-RAY DIFFRACTION23chain 'B' and (resid 408 through 417 )
24X-RAY DIFFRACTION24chain 'B' and (resid 418 through 444 )
25X-RAY DIFFRACTION25chain 'B' and (resid 445 through 465 )
26X-RAY DIFFRACTION26chain 'B' and (resid 466 through 475 )
27X-RAY DIFFRACTION27chain 'B' and (resid 476 through 500 )

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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