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- PDB-8arp: Crystal structure of DEAD-box protein Dbp2 in complex with ADP -

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基本情報

登録情報
データベース: PDB / ID: 8arp
タイトルCrystal structure of DEAD-box protein Dbp2 in complex with ADP
要素ATP-dependent RNA helicase DBP2
キーワードHYDROLASE / helicase
機能・相同性
機能・相同性情報


nuclear polyadenylation-dependent mRNA catabolic process / SUMOylation of transcription cofactors / G-quadruplex DNA binding / alternative mRNA splicing, via spliceosome / ATP-dependent activity, acting on RNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / snoRNA binding / termination of RNA polymerase II transcription / Estrogen-dependent gene expression / rRNA processing ...nuclear polyadenylation-dependent mRNA catabolic process / SUMOylation of transcription cofactors / G-quadruplex DNA binding / alternative mRNA splicing, via spliceosome / ATP-dependent activity, acting on RNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / snoRNA binding / termination of RNA polymerase II transcription / Estrogen-dependent gene expression / rRNA processing / G-quadruplex RNA binding / RNA helicase activity / RNA helicase / ribonucleoprotein complex / mRNA binding / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytoplasm
類似検索 - 分子機能
DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. ...DEAD-box subfamily ATP-dependent helicases signature. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent RNA helicase DBP2
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.05 Å
データ登録者Song, Q.X. / Rety, S. / Xi, X.G.
資金援助1件
組織認可番号
Not funded
引用ジャーナル: J.Biol.Chem. / : 2023
タイトル: Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities.
著者: Song, Q.X. / Liu, N.N. / Liu, Z.X. / Zhang, Y.Z. / Rety, S. / Hou, X.M. / Xi, X.G.
履歴
登録2022年8月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年3月22日Provider: repository / タイプ: Initial release
改定 1.12023年5月24日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume
改定 1.22024年2月7日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: ATP-dependent RNA helicase DBP2
B: ATP-dependent RNA helicase DBP2
C: ATP-dependent RNA helicase DBP2
D: ATP-dependent RNA helicase DBP2
E: ATP-dependent RNA helicase DBP2
F: ATP-dependent RNA helicase DBP2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)369,89923
ポリマ-366,4946
非ポリマー3,40517
00
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)145.939, 168.843, 168.870
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
非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
1given(0.442537864414, 0.871554071838, -0.211077564942), (0.0487202603946, -0.258400488357, -0.964808542584), (-0.895425359696, 0.416680558077, -0.156814341609)12.6536528518, -2.78756477108, 15.9004439654
2given(-0.454577702365, -0.87676834361, 0.156959817009), (-0.879812899729, 0.414514255509, -0.232609530007), (0.13888259064, -0.243834377442, -0.959821036649)-46.8786902571, -22.6218294788, 39.1957687527
3given(-0.998750139657, 0.0252397783766, 0.0431406087306), (0.0451280848142, 0.0843477110898, 0.995413943842), (0.0214852157341, 0.996116668479, -0.08538131109)-35.8468372866, -37.5083322527, 42.5884554273
4given(-0.998608892362, 0.0488168337149, 0.0199297978367), (0.0256173152258, 0.118803597408, 0.992587254806), (0.0460872352867, 0.991717007008, -0.119888885034)-34.9916601046, -36.7805883159, 42.9155918485

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要素

#1: タンパク質
ATP-dependent RNA helicase DBP2 / DEAD box protein 2 / p68-like protein


分子量: 61082.387 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
: ATCC 204508 / S288c / 遺伝子: DBP2, YNL112W, N1945 / プラスミド: pET21a HMT / 発現宿主: Escherichia coli K-12 (大腸菌) / Variant (発現宿主): C2566H / 参照: UniProt: P24783, RNA helicase
#2: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 6 / 由来タイプ: 合成 / : C10H15N5O10P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: ADP, エネルギー貯蔵分子*YM
#3: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 8 / 由来タイプ: 合成 / : SO4
#4: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 3 / 由来タイプ: 天然 / : Mg / 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: 2.82 Å3/Da / 溶媒含有率: 56.46 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 / 詳細: 2.02 M (NH4)2SO4 100 mM Tris pH 7.0 150 mM Li2SO4

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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: SSRF / ビームライン: BL17B1 / 波長: 0.9793 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2019年12月23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: 0.9793 Å / 相対比: 1
反射解像度: 3.046→119.4 Å / Num. obs: 1019758 / % possible obs: 96.2 % / 冗長度: 13.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.044 / Rrim(I) all: 0.159 / Net I/av σ(I): 15 / Net I/σ(I): 11.2
反射 シェル解像度: 3.046→3.099 Å / 冗長度: 13.4 % / Rmerge(I) obs: 1.284 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3975 / CC1/2: 0.688 / Rpim(I) all: 0.362 / Rrim(I) all: 1.355 / % possible all: 100

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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
PHENIX1.20.1_4487精密化
autoPROC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
開始モデル: 8ARK
解像度: 3.05→119.4 Å / 交差検証法: FREE R-VALUE / σ(F): 4.92 / 位相誤差: 29.3155
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2704 3782 4.89 %
Rwork0.2226 73508 -
obs0.6542 77290 96.2 %
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: 110.1 Å2
精密化ステップサイクル: LAST / 解像度: 3.05→119.4 Å
タンパク質核酸リガンド溶媒全体
原子数21089 0 205 0 21294
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.004621710
X-RAY DIFFRACTIONf_angle_d0.997829435
X-RAY DIFFRACTIONf_chiral_restr0.05383227
X-RAY DIFFRACTIONf_plane_restr0.00933850
X-RAY DIFFRACTIONf_dihedral_angle_d10.71362981
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.10.72231790.71723795X-RAY DIFFRACTION95.5
3.1-3.150.72111870.71983742X-RAY DIFFRACTION95.24
3.15-3.220.71232340.72323758X-RAY DIFFRACTION94.14
3.22-3.280.74711700.72413799X-RAY DIFFRACTION95.72
3.28-3.350.72861660.72273775X-RAY DIFFRACTION95.79
3.35-3.430.73381790.7283826X-RAY DIFFRACTION95.53
3.43-3.520.73431820.73243819X-RAY DIFFRACTION95.45
3.52-3.610.74512410.73293729X-RAY DIFFRACTION93.93
3.61-3.720.74891720.73073793X-RAY DIFFRACTION95.66
3.72-3.830.72461940.72073591X-RAY DIFFRACTION89.31
3.93-3.970.7112650.70451121X-RAY DIFFRACTION28.18
3.97-4.130.70321950.70943832X-RAY DIFFRACTION95.16
4.13-4.320.69281830.69863796X-RAY DIFFRACTION95.4
4.32-4.550.68442300.68223800X-RAY DIFFRACTION94.29
4.55-4.840.66661810.66633836X-RAY DIFFRACTION95.49
4.84-5.210.63692110.63533798X-RAY DIFFRACTION94.74
5.21-5.730.58012240.58873841X-RAY DIFFRACTION94.49
5.73-6.560.55891540.55833918X-RAY DIFFRACTION96.22
6.56-8.270.5842120.57233905X-RAY DIFFRACTION94.85
8.27-119.40.61632200.56884037X-RAY DIFFRACTION94.28
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)
12.420858808420.1340475840672.484028346513.57246476386-1.660084526174.153762656730.0893137890221-0.863153890321-0.04931199110470.01708928151310.2778916050990.282858930634-0.194994564987-0.31260302394-0.4602544319270.6221752502330.149176428733-0.03204963619550.968070221449-0.2357245377450.542785483918-46.15131224660.8881615457344.3621861551
21.401965730680.9074824226790.6416527280930.6401758590170.4540363591190.322420875883-0.865378495827-0.261898078111.03080791849-0.1316210244990.1304674175630.914738096828-0.709343023299-0.4612711289510.5996936570720.8404119730810.307550316862-0.4936830216391.19159319101-0.1737856363161.48554947805-69.199488569117.493399905122.8110893212
30.418703482419-0.4609462079390.1291673776353.202282954330.811617493231.66550200632-0.361558347586-0.2050946427990.4883720142790.2756180167570.1365530597220.0231738660037-0.0392451153965-0.1570387473240.2022581614220.4229232495210.208603473572-0.08872637405380.726693186594-0.1996596117430.796423773741-47.42938013843.7952814866826.3214825828
40.498557401762-0.332795026383-0.6561412443623.717165354910.04737431266151.0302173928-0.156738567654-0.662075070486-0.1141374851840.777712505878-0.0003701920011290.5724522626420.121208002704-0.2541553860010.2886864225390.5700873069990.2919551985690.02936392172030.983068468726-0.05828436197010.62465309927-58.3616371781-3.3767201871634.3141402796
50.1427916399810.4188828428790.5443255354791.583028449150.9606725765263.436414422770.4172446404220.410755878931-0.604390515639-0.220112343105-0.4331763183260.228706335139-0.119360404017-0.287054891743-0.02121579980560.3370105447620.144469201616-0.05158559134510.707073080479-0.1948757109150.877252217703-57.3859615322-19.07944550191.94863109307
63.50768291255-0.310588975479-0.8240394550692.420987925930.3450731050890.42953727092-0.3328400034740.270097179399-0.06875790744720.1498957915060.400748496526-0.2850710421460.37918587039-0.201194634961-0.04946072057210.2695326420940.12563167491-0.0371840380530.768674518698-0.1084595877860.821942996242-44.4465379133-15.85706830221.4177712865
72.757014466920.615340350298-1.038509404327.926914551451.98880094581.70430550796-0.4260202052040.07002969156660.81552825831-0.008551073512370.1049448948550.182785828273-0.05568262625070.3149899771370.4695613786640.3004797949490.0889510900716-0.03726657407850.5103638951230.01235767446950.850167193734-42.2594070107-5.850182552670.3633300633
83.46060984594-0.085807787101-0.6306622922283.01580977279-0.3450418624493.651385777670.2282288694520.1659971703960.5439244931460.1819713425860.09423164207360.280071036043-0.442345259414-0.563681998358-0.06251250416590.3330191225140.000187691761444-0.02460758518740.581764963303-0.1469304115060.772148695469-55.5199674872-9.964504609445.78075704384
94.818037671630.640329955876-0.7687595468292.588364569871.168916831841.458149664310.192437367892-0.00764665981985-0.293098313516-0.242765748478-0.2339763425420.95411607475-0.0371203110869-0.748373205660.09508807858270.3117807002750.004405517940730.01778679709710.630161242202-0.1925777835840.940926532986-64.6576669906-19.75067615737.51964051934
101.733702402191.479300875271.067091738761.687691824180.1443234709992.041039166180.523565422276-0.9115525313440.4587323869540.646477682935-0.796851852680.2728897698840.874260125305-1.189286077560.3529882148880.8627365657450.03231994416820.06532158720911.29796296416-0.1419983542690.87126806255-11.2984451367-40.507039188665.9054206366
110.9095246857050.240449996785-1.118476243361.9765636511-0.1940627235851.63613913395-0.0236939809333-0.5911648500610.1408254860660.0220459930482-0.1907018076510.733634828927-0.132808264415-0.3205466731760.1957629224380.7832772735420.565094234646-0.2029734677612.06742542215-0.4560005314971.09855201915-1.03474985182-32.311476265370.1735720631
123.4187948939-0.01933008801661.025802375840.8936003625570.1726307295871.048160880380.114587283983-0.8177127366950.52593517820.10689701778-0.0203917232145-0.192540173545-0.285874609827-0.259214623290.04106664738490.6380852958330.439664989584-0.03264094978691.21779535323-0.158625360471.08439012347-8.75960712603-29.473247766757.3727300633
132.69107793023-0.105659558605-0.9082669063873.306162273691.748533987322.78482633653-0.650982189997-0.641179729469-0.1189503332160.1338658728050.7731635299021.161277497820.4748676591730.320699757687-0.149359806620.6857373235230.214110193659-0.1303310387560.9120636437620.1817077153371.08360148215-17.3700268856-33.106495931148.4897295744
140.3983581067640.395127070546-0.2004639809150.848175431566-0.3188705488251.01856140786-0.24686375289-0.869045286109-0.1250981932530.45686929152-0.127216827146-0.360472847743-0.109514045102-0.6462430554310.2102093901020.7546416984630.310209828833-0.007819893077581.427941368790.03109304028480.994664009985-26.0007036687-22.556652915461.0795718432
151.39838603586-0.6220578047240.006071162758441.037130338460.3549477848170.334838546649-0.206071649273-0.6796513819830.2649368992660.3932075371030.610676018484-0.381368918466-0.1403869802110.04050674866180.4748718921120.5932221045340.747395430586-0.287748127391.40819785653-0.713156468131.28884868615-16.4055012544-2.1050029368550.6817928011
161.034163097390.655590930632-0.7489572153572.86553191255-0.9340743949520.626976762494-0.404568551302-1.392382016960.132637522176-0.0443885027222-0.451150762155-0.231575023538-0.268456847254-0.7451522525330.6981856040410.9970805968410.71630440498-0.246580990361.99973383587-0.4162500841020.926613751092-22.0621467879-8.0875422965161.2130470535
170.0502354107984-0.1125843202520.1279498401042.159755049360.6718795910662.253573024410.115807081748-0.423911676514-0.2053353969570.005329000706220.0688345553839-0.459589821724-0.0693769153046-0.0823445742072-0.2496847952750.78673830750.247462155347-0.06282660126851.23447006243-0.2136339360531.21018160521-35.587927957-8.2702043437765.1955287079
181.713782764070.4548570086311.28986739081.79832776602-0.3106119349321.25214319001-0.3625441800470.0926753524276-0.2349442624340.2136501049540.2664891143380.28223626315-0.0933091280866-0.1781222927160.1596978646790.1776244194740.0820017450934-0.05528058805550.956207315087-0.05258902294141.37331291274-43.6900877382-48.44759794552.7098843538
191.670292519051.45471407908-1.022401992491.5933341373-0.8137753253511.737147072110.0805358789961-0.319297523661-1.86681405286-0.245530363786-0.123989405637-0.4800517748760.783101773767-0.1375372233010.02075533609040.6004302655310.005756602463610.03149045463150.945599898008-0.02611955574121.80466392862-31.1329459765-65.5506652866-1.53510635004
201.13617210609-0.4269289943690.9181015241920.160702897199-0.3450667489330.7423403762820.140012839333-0.178896228588-1.014589231770.1254173704660.0876521671840.4196330739350.2926801347820.351506247221-0.1161753355240.2905267628180.0959336854244-0.002778080264010.6555496283050.2107665438641.85115592518-31.2444759975-61.2903073264.56705748723
214.27690824707-1.84598375442-0.1568194196052.300801208140.1118656397331.37971147655-0.065553150937-0.943509634651-0.7352488671080.5228975217460.4086666336540.242361362620.159412094216-0.00643687078659-0.2039985957630.1672540779870.0301276788278-0.06828192192440.7793702001620.1680486638591.14370802723-33.1489804223-43.22829346789.88467273214
221.46304145374-0.713720809877-0.3826099006710.4220540725870.2929825559120.2504837327410.0267806675564-0.239551113974-0.6340021763330.484225142629-0.171211985183-0.1665576910810.2245741619370.01331287800630.2151462837150.540708375919-0.199562228374-0.02237054416331.060883586070.4163107460331.91025226719-36.7791747008-63.827459645317.3998228573
231.120090234230.3433045662070.9814471683851.189582071651.345483268762.229501457670.449483937712-1.13390530715-0.1280102328130.3849271319290.266200491499-0.008642176954250.195118249346-1.27876700621-0.707351687830.4495173397890.0808144858887-0.08340110088191.313159695970.4290810286381.3117764212-8.80110305354-53.40147432829.0858516649
241.293963136870.1251562874220.1129580048020.397506716775-0.3310929962641.608845694520.380616299752-1.00243412089-0.5933607201940.2278522254210.3183469998810.263132122640.357758191459-0.704383322799-0.1603468464550.227096605326-0.0434427939783-0.09506851879861.15077620710.6010842099931.2815912878-10.5546820449-57.998278966420.0286087591
250.7981223961870.325048477056-0.2958780864421.88934391106-0.1249765577491.74149754608-0.741209472079-0.2881731072020.2106866868070.2620518977970.4671983795350.1879843201810.3446636032690.1800069183320.1733076203280.719035465636-0.3661541564910.04104179370062.009404630470.4722537184821.36363605312-21.2342102413-67.231354989433.800709516
261.798894672310.263726867760.9731697967630.405855248229-0.5677848128711.83791092184-0.2154213709220.04789994326050.416929881734-0.408867648270.097300345225-0.896930311439-0.825529447960.6369857188230.1077386216541.00512402528-0.3132960212550.26993696570.753662352885-0.2215689682321.50969712331-28.067000740425.68390215772.58392010194
271.97303874521-0.8477108481870.7082808493290.525621027065-0.5757992669622.255339420950.2210684238120.1313648047770.7981735970520.354480365524-0.136830753044-0.167645321119-0.6946803091430.484213104911-0.001674207258670.657318862438-0.1612405900080.1073648903740.590954537231-0.1170197868471.30580018146-21.089908666610.99579340586.60864960651
280.02549568510870.10360112840.006581569451040.662625596310.06060527485550.00528529950979-0.139740101437-0.07178732687380.705962970531-0.5312550896110.532205282152-0.6011940144330.02469309790680.307560940767-0.2024101881990.699632918257-0.194259156660.2459106276071.2620076956-0.294006613641.46861653203-7.4094210064524.781374974316.0232289009
290.688801001053-0.0646450755227-0.03133425063230.862814279899-0.1990487243131.77834514918-0.3809733017530.284034882190.0118999074770.0486983175510.033641643267-0.800558802282-0.4986721510630.2803142013140.4843948289860.488582243177-0.131211164214-0.3588123586471.01307342171-0.6471862195621.91323964385-10.27817871517.251485950233.0512317768
302.34392727308-0.5816931389012.193925447860.8630195198460.371837705136.45736658428-0.205843345956-0.4703709675711.558691919470.373760988274-0.583484824558-0.505494141914-0.0162736723705-0.04273961563760.7793358754681.113294808880.101540067478-0.4922330721571.04847834065-0.6002455531561.6812035254411.31800442544.2269369682239.5000284929
311.788442197320.984050269357-1.187354911651.50669074805-1.622399761871.79835921986-0.464636868846-1.17574434518-0.1976485783710.454265375731-0.424556874886-0.73047741234-0.3617363324540.432900094194-0.01384321366380.4889885531030.403990238773-0.4417291858541.49697083211-0.7317517219931.4957829648321.830544297-15.130431992953.6289836114
320.886202451068-0.04028920395590.9580780495230.333919684601-0.1251908850386.084861586040.293718253193-0.3435005520920.139152710620.4210145004840.354326962794-0.107875714337-0.146223851687-0.548825906747-0.4341826010630.8038359111010.321248783457-0.415816525680.860878992523-0.5252131503091.460661159626.1324601534-17.262429095439.7667858407
332.9600085872-1.338219277011.010845149691.75122924636-1.316141892910.980974321008-0.221701341166-0.9503952404950.209420379857-0.1387501640990.29554762271-0.409999899654-0.506138450904-0.154774869007-0.09570753589220.6651845807520.104294265886-0.3024227538510.813262064394-0.4989084655821.451556592348.2796906457-9.4479239568234.3055996079
340.1256323337180.263072924401-0.44532130031.92006677173-0.03654189945542.06931883812-0.30769502259-0.666463006891.06234768783-0.03091816764710.0496013175956-0.479377583523-0.1523996523970.6148310844360.04577934195990.6779807770010.0248988612605-0.3245030678141.12172922418-0.5304312389661.651524998125.0805031804-11.48322917435.803971102
353.42059217729-0.0584979137204-0.5054544144181.65822161804-0.5403215780923.64235240913-0.41927129362-0.4488695951190.04455866142950.1315054092680.478326778109-0.02710444263050.0525869778355-0.257736697516-0.2086586735470.3016898507960.239365840485-0.1565631963740.681077467199-0.13696235360.97167612163912.283536735-39.289098094728.6825233623
364.33097388166-1.413064553841.328529174960.643520310108-0.0808313222112.80481508292-0.029138719098-0.3856529365070.296095637628-0.0380060759556-0.0618933835685-0.243033624936-0.4277702118040.9357919033420.1197694350960.253605435552-0.1295604935140.02639159386030.916973220327-0.450115361151.1999578333228.4748303026-33.93225340621.2960573273
372.11527869504-0.4956716519640.8463225117382.017574230420.7211134210313.639886205150.2443135977870.430396599312-0.00527003137604-0.0910950966247-0.0279944279373-0.1081698644150.2464142416780.610014516277-0.08644355386210.2741844878570.1611043730590.02947685115560.567803442481-0.1603909619691.257242899457.0429124026-42.0545976648-8.49599272758
383.46821054251-1.23370477931.446238010553.681154879080.678284412742.110403378310.05784824588160.7881123567440.40634830139-1.23664366849-0.158025097230.3098493981-0.162570765065-0.531731513401-0.04560106076740.834409381740.149656406867-0.1947288467770.620819721854-0.0411923973850.738477007937-7.82100844749-46.6402829664-22.7932408729
391.99234555188-0.5517563899930.2978632944922.40929616868-0.02480847941192.826152247090.1245503279740.4065027387130.361073436062-0.256104384634-0.140358593783-0.161719945655-0.2830634718320.1060362779790.0006873503158580.2534375557740.08470434398210.03129419677140.619752853102-0.03450094944280.98408657415-3.88931513155-33.7547137738-5.22913855713
401.242532719460.118709337141-0.5378281226660.286583514801-0.6289099719972.1036501160.4329871686280.5304772375980.235343264609-0.337470844822-0.291910588517-0.654444920731-0.51668483539-0.135054592761-0.1935056741720.5925044611670.1677868949010.2722798876310.6919499529170.1635850204181.00593339128-23.1331722374-20.0094267347-16.5653051094
414.51334590681-0.697490116869-2.489191029013.45246418984-2.541982838385.280978629650.05209040194980.371829065887-1.042469923140.241370959413-0.741025825957-1.14704588992-0.1154951157680.6651275199090.5750803196510.6968014512720.1705131999430.2200069715720.9183609347080.3421515930011.14687638372-17.4585145334-11.7600481765-29.120795841
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 53 through 79 )AA53 - 791 - 27
22chain 'A' and (resid 80 through 104 )AA80 - 10428 - 52
33chain 'A' and (resid 105 through 277 )AA105 - 27753 - 225
44chain 'A' and (resid 278 through 320 )AA278 - 320226 - 268
55chain 'A' and (resid 321 through 357 )AA321 - 357269 - 305
66chain 'A' and (resid 358 through 383 )AA358 - 383306 - 331
77chain 'A' and (resid 384 through 416 )AA384 - 416332 - 364
88chain 'A' and (resid 417 through 450 )AA417 - 450365 - 398
99chain 'A' and (resid 451 through 495 )AA451 - 495399 - 443
1010chain 'B' and (resid 53 through 104 )BC53 - 1041 - 52
1111chain 'B' and (resid 105 through 128 )BC105 - 12853 - 76
1212chain 'B' and (resid 129 through 228 )BC129 - 22877 - 176
1313chain 'B' and (resid 229 through 277 )BC229 - 277177 - 225
1414chain 'B' and (resid 278 through 356 )BC278 - 356226 - 304
1515chain 'B' and (resid 357 through 416 )BC357 - 416305 - 364
1616chain 'B' and (resid 417 through 450 )BC417 - 450365 - 398
1717chain 'B' and (resid 451 through 496 )BC451 - 496399 - 444
1818chain 'C' and (resid 52 through 90 )CE52 - 901 - 39
1919chain 'C' and (resid 91 through 131 )CE91 - 13140 - 80
2020chain 'C' and (resid 132 through 164 )CE132 - 16481 - 113
2121chain 'C' and (resid 165 through 298 )CE165 - 298114 - 247
2222chain 'C' and (resid 299 through 330 )CE299 - 330248 - 279
2323chain 'C' and (resid 331 through 397 )CE331 - 397280 - 346
2424chain 'C' and (resid 398 through 450 )CE398 - 450347 - 399
2525chain 'C' and (resid 451 through 496 )CE451 - 496400 - 445
2626chain 'D' and (resid 53 through 148 )DG53 - 1481 - 96
2727chain 'D' and (resid 149 through 302 )DG149 - 30297 - 250
2828chain 'D' and (resid 303 through 343 )DG303 - 343251 - 291
2929chain 'D' and (resid 344 through 496 )DG344 - 496292 - 444
3030chain 'E' and (resid 53 through 79 )EI53 - 791 - 27
3131chain 'E' and (resid 80 through 188 )EI80 - 18828 - 136
3232chain 'E' and (resid 189 through 228 )EI189 - 228137 - 176
3333chain 'E' and (resid 229 through 277 )EI229 - 277177 - 225
3434chain 'E' and (resid 278 through 332 )EI278 - 332226 - 280
3535chain 'E' and (resid 333 through 450 )EI333 - 450281 - 398
3636chain 'E' and (resid 451 through 496 )EI451 - 496399 - 444
3737chain 'F' and (resid 54 through 90 )FK54 - 901 - 37
3838chain 'F' and (resid 91 through 137 )FK91 - 13738 - 84
3939chain 'F' and (resid 138 through 302 )FK138 - 30285 - 249
4040chain 'F' and (resid 303 through 450 )FK303 - 450250 - 397
4141chain 'F' and (resid 451 through 496 )FK451 - 496398 - 443

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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