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- PDB-6oat: Structure of the Ganjam virus OTU bound to sheep ISG15 -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 6oat
タイトルStructure of the Ganjam virus OTU bound to sheep ISG15
要素
  • Interferon stimulated gene 17
  • RNA-dependent RNA polymerase
キーワードHYDROLASE / DUB / deISGylase / Innate Immunity
機能・相同性
機能・相同性情報


viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription
類似検索 - 分子機能
Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / Cathepsin B; Chain A / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Ubiquitin family ...Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / Cathepsin B; Chain A / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
類似検索 - ドメイン・相同性
prop-2-en-1-amine / RNA-dependent RNA polymerase / Interferon stimulated gene 17
類似検索 - 構成要素
生物種Ganjam virus (ウイルス)
Ovis aries (ヒツジ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.17 Å
データ登録者Dzimianski, J.V. / Williams, I.L. / Pegan, S.D.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI109008 米国
引用ジャーナル: Plos One / 年: 2019
タイトル: Determining the molecular drivers of species-specific interferon-stimulated gene product 15 interactions with nairovirus ovarian tumor domain proteases.
著者: Dzimianski, J.V. / Scholte, F.E.M. / Williams, I.L. / Langley, C. / Freitas, B.T. / Spengler, J.R. / Bergeron, E. / Pegan, S.D.
履歴
登録2019年3月18日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年1月8日Provider: repository / タイプ: Initial release
改定 1.12023年10月11日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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: RNA-dependent RNA polymerase
B: Interferon stimulated gene 17
C: RNA-dependent RNA polymerase
D: Interferon stimulated gene 17
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)75,1146
ポリマ－74,9994
非ポリマー1142
水00
1
A: RNA-dependent RNA polymerase
B: Interferon stimulated gene 17
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,5573
ポリマ－37,5002
非ポリマー571
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: RNA-dependent RNA polymerase
D: Interferon stimulated gene 17
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,5573
ポリマ－37,5002
非ポリマー571
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)55.388, 55.388, 497.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61

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要素

#1: タンパク質 RNA-dependent RNA polymerase


分子量: 20052.535 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Ganjam virus (ウイルス) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A191KWA2
#2: タンパク質 Interferon stimulated gene 17


分子量: 17447.154 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Ovis aries (ヒツジ) / 遺伝子: ISG17 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9GKP4
#3: 化合物 ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE / アリルアミン


分子量: 57.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H7N

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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: 3.09 Å3/Da / 溶媒含有率: 60.24 %
結晶化温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1 M MES pH 5.5, 15% PEG 20,000

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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: APS / ビームライン: 18-ID / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2016年12月9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 Å / 相対比: 1
反射解像度: 3.15→50 Å / Num. obs: 12288 / % possible obs: 85 % / 冗長度: 6.7 % / Biso Wilson estimate: 97.7 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.074 / Net I/σ(I): 11.2
反射 シェル解像度: 3.15→3.2 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1139 / CC1/2: 0.662

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
PHENIX1.16_3549精密化
HKL-2000データ削減
HKL-2000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: 6OAR

6oar


解像度: 3.17→41.44 Å / SU ML: 0.5909 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 37.1458
Rfactor反射数%反射
Rfree0.3042 1237 10.11 %
Rwork0.2506 --
obs0.2562 12240 83.82 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 117.52 Å2
精密化ステップサイクル: LAST / 解像度: 3.17→41.44 Å
タンパク質核酸リガンド溶媒全体
原子数4912 0 8 0 4920
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00275016
X-RAY DIFFRACTIONf_angle_d0.616780
X-RAY DIFFRACTIONf_chiral_restr0.0432756
X-RAY DIFFRACTIONf_plane_restr0.0042884
X-RAY DIFFRACTIONf_dihedral_angle_d12.06873000
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.290.37561280.36721144X-RAY DIFFRACTION77.66
3.29-3.440.38751460.36291253X-RAY DIFFRACTION85.3
3.44-3.620.39831480.3431289X-RAY DIFFRACTION90.49
3.62-3.850.36971350.3081266X-RAY DIFFRACTION85.58
3.85-4.150.31661400.28521253X-RAY DIFFRACTION87.23
4.15-4.570.3391300.2571199X-RAY DIFFRACTION80.84
4.57-5.230.28631380.23611236X-RAY DIFFRACTION85.71
5.23-6.580.32261380.25411210X-RAY DIFFRACTION83.52
6.58-41.440.22991340.16871154X-RAY DIFFRACTION78.58
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)
16.087921299613.31214857161-4.53421551014.6646625048-6.215334455028.292957830760.5589497447350.2511606852260.6807175407981.731751198480.197641033512-0.712426937-1.61529271330.622306406992-0.7839240723081.127117824980.173316281716-0.1140369719441.52274112189-0.6879185250931.9469580699815.270731971216.0695370904-3.59099535353
29.462849087060.646343786812-2.682025146976.194602388854.324594380074.058159006370.8085240331390.594592139965-0.2163326785820.108877482562-0.881357827862-2.2342760586-0.576701347015-1.894201067040.1580268892211.347987121920.622088529595-0.1568399238292.113339606120.5480118105791.2635122487510.38204025496.02986042509-8.62200053989
36.4430307825-6.38845778120.5120000039387.65846689952-2.599836021478.7121960588-0.398074679412-0.1199967116191.86687981088-0.679616863015-0.358531848089-2.327954108560.5761030198550.0895272974280.7739581957351.448678177310.516882007055-0.3783853427410.921637437491-0.345733823891.333692165853.203829967194.71745854004-13.8580962985
40.0996107595541-0.0809491697193-0.06978837453180.2944887890160.1865464710820.111554009840.2361086331890.5112499139130.15743598831-0.55787133229-0.364887953179-0.1693036447380.1737202241890.1000103500470.2651329627840.4235402311321.16188601367-0.1729698200991.77329642543-0.1496511979141.320953708048.578708655256.960945346480.335516984225
51.540226866552.804689402090.3551366016699.30344241929-3.8872984265.10901674305-0.647002761628-0.257546430177-0.6187474761550.9573683368971.10050959581-1.6855089837-0.255746958403-0.747339156259-0.3066583918991.11578028749-0.187191160293-0.3030555636131.104324700380.1799356703060.8938903192796.6396407979618.58587770855.97542526039
67.760319288178.385890046930.09684619802329.87349836441.126452530659.068371332750.352454349956-0.5614399137850.632094130832-0.533256460574-0.670784573547-0.75322291041-0.8173923404130.01632458041730.5876175211950.7267761130470.218348323916-0.07886650085920.6319419651750.02328263948850.961798269502-10.307768244919.90969116513.78969443414
74.9075178556-2.28657950457-3.589919221434.804682983190.8069204653982.84177604820.5556637192510.7918348677810.884368615036-0.862367167328-0.317076351429-0.736742649696-0.306091073114-0.852550087543-0.1573473902361.575016420250.501954839129-0.1750327448660.8195628174480.004170522597220.759281484589-10.455315386818.3718719727-3.80339291677
84.127151742720.0157793885514-2.824317513384.97226145364-3.441147660334.307874963511.032706243150.607315790875-0.275168122404-0.3302980324831.421497964840.359825743289-0.4967512784650.0259824774122-1.52366002391.38123107117-0.293679227645-0.4795010720960.7152974921110.2210245087831.30961310207-4.9734411144426.5213517127-6.79959834742
93.256970419830.4364781157971.490349539332.092679341643.279650722955.63163199786-0.09641135365540.5448320016320.356731266488-0.6795041790890.2976962997270.790368304134-2.95071652605-0.270459063551-0.01099710417911.6999882340.173569425876-0.2969824781390.9903303478770.003467501336981.07440275049-13.548812407926.4413160971-5.40985926829
102.9599110204-0.4196918309831.292790317280.743040134203-1.240478999522.185657569180.6404578371590.4711158453610.292592796227-0.7576858035150.5523786295180.471634785250.87005893313-0.0257567834840.6595826283372.283429574721.00054018786-0.5835782325840.739793021350.09760763038930.887473421667-13.839876253717.0156697608-17.5400984328
112.794174094631.610943206792.397513221118.44715749387-0.7180563294753.06219772558-0.4162281771970.2450589850880.0394535705818-0.5657952290611.79249589607-0.5614145712850.913783813225-0.114522775901-1.308095200271.249072176610.08868949184280.2265936031660.6473677885280.01906303426021.18098104431-10.19081709388.76508245711-21.5559055951
127.09713306361-1.961714789215.721509092749.495353711071.713539406188.505943072940.0558228131596-0.3668473724630.1882780971862.400842397860.712377059496-2.209435931011.64438356726-0.491273037251-0.7901722709751.398539916950.242989038248-0.256494798880.746807933371-0.07942051871591.08512740116-10.50594912981.48090145294-16.1536724904
130.041190937664-0.4716232585720.01473137287384.66055621148-0.05386585522511.13311100750.2791354735160.205028334209-1.003871782390.01725403599450.4350121907012.467632911740.326721201605-0.105835253743-0.301888343812.574702836591.02914045482-0.8354567623050.833520101198-0.2769139245691.46183181831-20.37538241229.49729095841-14.3965054998
141.858319634861.16679668892-1.9140612120.796968087267-1.647757157135.327269441290.0709531132869-0.6801772256870.08906930132720.8803118882120.619900306292-0.318575442768-0.5392693674640.497250712903-0.5814122410971.653425024271.17118836235-0.2347090458551.16084723671-0.211367457690.858261434635-15.659329155912.1948562765-4.26327853485
154.122847258741.954469374070.1910909146982.690079703422.625706360923.6494680683-0.748940749896-0.15424042311-0.429259152994-0.473413393630.40237153991.40397663252-0.631304507608-0.01171856067290.4223094402011.586485595150.462824579608-0.4526384355830.2753826053520.003475425868931.34595896739-7.3793394389611.4778019272-12.9434696601
165.057228685193.50538597384-1.946617858984.40060183256-4.206604938554.902427397811.203745120420.967356346090.938930296089-2.458304422310.751372295609-1.12630188447-1.5346309146-0.370237036146-1.57904494652.11963527121-0.3135754278550.3929047806290.703404544711-0.05826039992490.933822307168-3.1991944732916.9868570958-18.1130715458
172.608115426961.52615510952.431244967417.582410883912.883771367993.15852007319-0.190352421366-0.62076777407-0.034778683441-0.8086673181361.66869417973-0.802980938951-1.077360839020.813450796302-1.14441596880.8995289718620.06681472324760.06269536893520.931529288841-0.02968110696560.9632081527241.1506522096511.9636593487-2.2094157484
182.667597879460.4417495878082.011230726795.22838560264-5.440317840378.1779868382-1.148901545670.3066400107810.454894090619-0.0388201398707-1.04685060525-1.41607042199-0.176496979658-0.4104548071751.830291259881.017503444520.339384988263-0.07632469836490.645537054433-0.2172574705951.153838134313.496222678699.40421804032-1.4033663298
194.75144992485-3.66015346739-1.032864548552.904565286141.502796229537.41657511271-0.11515376062-0.6346065894110.4776873576340.4863528358160.347635971945-1.80001578883-0.95641036681.40648936391-0.09159025785790.842831611705-0.1201260463660.001599433424450.712400034209-0.05494469946271.06625465197-1.5704032132814.8292232756-1.04989054502
205.96722054732.13831294794-2.002844416073.91668850155-1.596644627322.61338782477-0.1146870216580.7948258026392.355770688410.2476117696430.0134625414091-0.5465741134030.3231960202820.1573296463530.2255574320461.19624167932-0.596320568647-0.2304142465391.32020631133-0.07137649472451.780134354465.7293566038624.4775000620.478330012421
219.35756488805-2.205711072172.419506050619.56447545402-0.9657768145680.680653403677-0.1448345276821.558223507870.0925799771074-0.6156462306560.188412585451-0.7560472270370.7928370956950.1128735548830.06216506744282.098285724870.3776154625060.02297339348881.40840748544-0.1710316202330.9371867045228.63162252994-29.8778146644-37.7598744983
228.05632174056-1.875473297620.5904588982153.030210517941.362191567165.575589986580.6881485297941.02819014505-2.368539993922.1731047645-0.7432579587650.9533339167180.5212122319540.4850020001450.1575642403162.074883724230.536482275894-0.1785175939561.00027940971-0.3026083439951.290796671765.48394653251-36.1838862719-30.1536962402
239.43614372680.490171761494-3.484768676390.8796260672080.06001253723772.452371624941.206611002851.419866633891.049684879930.02599285809460.440232216836-0.04378620701931.35683813188-0.854950786288-1.852469027841.796250886860.13794458876-0.2796940149191.217801916710.2984710446041.150447988946.43040381336-21.5498159385-40.566167857
246.800640510925.339346668475.571748931748.01178534562.722318433178.659170786830.6044807449951.25304662652.54284938167-0.0958809260381-1.061410780831.17145761381-0.2812411776510.338537394910.495095597622.602489389190.353001339218-0.1455369239870.8700342807620.1063365638411.18308133241.83889020748-20.5609045762-32.0924898682
255.722085417645.342646658410.2708851006488.50252878875.729561662268.60039438279-0.9308847796321.793432801370.8272555514540.5051927053030.06835773072411.05037656159-0.898808797906-2.057701159750.9318427813151.063266732550.591563151815-0.1391390622491.65507488466-0.2776470495960.990270386966-2.58054441947-25.2555881512-25.7520219286
266.663303147961.2223687806-0.2261099336662.216857349220.1577326336731.971079760552.17660708518-0.170762674581-0.196948350861-2.65166958186-1.736920429882.64104110883-1.116491562030.55854349809-0.3517274109111.72821166956-0.0875383194141-0.3700816852371.05894509641-0.002374081797021.261868922676.68434230348-25.0814639779-23.4856923106
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754.79781422748-2.706410555364.524438952627.3840122155-2.43626984074.272185762091.229583887073.631803480980.351372034025-1.48078940439-2.619182177230.6824754265062.94835922779-1.763084214830.9942093886592.033686290360.2230711640530.4878574463372.13470827371-0.3215426707051.12109981988-47.04582634685.8130956628227.8397888952
762.39340475951.61817981631.037056420452.074640319771.042047466870.5676954275440.2146163124183.0190009246-1.36755469022-1.5484537536-0.5778073529990.9316209916020.3657246409760.22884411625-0.4573086903410.6840214348820.364677097387-0.3141938821242.64484794683-0.5989990084561.48528453782-39.76864982587.5388991872318.5503852066
774.60245855084-0.918721795374-4.305819920918.18241494798-2.703491195377.805132439140.2871879004571.66082359629-0.321874901196-1.71533295338-1.626635033490.2698497569630.94324643991-1.246638867381.352654839950.8187340866440.293350539697-0.03798359692771.7328795482-0.3643685171051.12080340308-30.97213968479.1378596212217.8297998438
787.768856356492.745994398171.562145371481.45726616228-1.572174743579.482176288261.01123386551.6500521424-0.856764504228-0.922543183101-1.457557782090.5279654057630.1721139129450.8182302054310.5608014821790.9549904244390.327128086959-0.1259175567251.40130974492-0.1709399707030.800194271494-36.572392982114.700062381730.7578587458
795.712330057761.93856207939-1.051514743670.674801772779-0.2611202305230.842443413614-0.2528655876610.25152855008-0.297378652272-0.418132908901-0.373883465928-0.0633429394801-1.08597935382-2.404391150650.57615265210.8363993656710.569195914970.002377071000412.06075003832-0.5434424340631.48878761654-43.483923888112.914177541430.8704371218
809.500293483-5.02351528931-7.162361689353.470340130332.474729503887.706835216220.0661578163510.602408665003-2.78970566726-0.364181398122-0.4896835251641.15619992220.287527676625-3.03458082250.0807389683650.4884430168890.0158504291643-0.3035857862111.200577500680.03396722410741.72553945948-29.205546623815.57875193321.1450564513
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:6)
2X-RAY DIFFRACTION2(chain A and resid 7:11)
3X-RAY DIFFRACTION3(chain A and resid 12:17)
4X-RAY DIFFRACTION4(chain A and resid 18:23)
5X-RAY DIFFRACTION5(chain A and resid 24:31)
6X-RAY DIFFRACTION6(chain A and resid 32:38)
7X-RAY DIFFRACTION7(chain A and resid 39:45)
8X-RAY DIFFRACTION8(chain A and resid 46:51)
9X-RAY DIFFRACTION9(chain A and resid 52:61)
10X-RAY DIFFRACTION10(chain A and resid 62:70)
11X-RAY DIFFRACTION11(chain A and resid 71:74)
12X-RAY DIFFRACTION12(chain A and resid 75:84)
13X-RAY DIFFRACTION13(chain A and resid 85:95)
14X-RAY DIFFRACTION14(chain A and resid 96:102)
15X-RAY DIFFRACTION15(chain A and resid 103:108)
16X-RAY DIFFRACTION16(chain A and resid 109:113)
17X-RAY DIFFRACTION17(chain A and resid 114:123)
18X-RAY DIFFRACTION18(chain A and resid 124:135)
19X-RAY DIFFRACTION19(chain A and resid 136:154)
20X-RAY DIFFRACTION20(chain A and resid 155:159)
21X-RAY DIFFRACTION21(chain B and resid 2:8)
22X-RAY DIFFRACTION22(chain B and resid 9:15)
23X-RAY DIFFRACTION23(chain B and resid 16:23)
24X-RAY DIFFRACTION24(chain B and resid 24:34)
25X-RAY DIFFRACTION25(chain B and resid 35:41)
26X-RAY DIFFRACTION26(chain B and resid 42:46)
27X-RAY DIFFRACTION27(chain B and resid 47:51)
28X-RAY DIFFRACTION28(chain B and resid 52:59)
29X-RAY DIFFRACTION29(chain B and resid 60:65)
30X-RAY DIFFRACTION30(chain B and resid 66:72)
31X-RAY DIFFRACTION31(chain B and resid 73:82)
32X-RAY DIFFRACTION32(chain B and resid 83:87)
33X-RAY DIFFRACTION33(chain B and resid 88:93)
34X-RAY DIFFRACTION34(chain B and resid 94:105)
35X-RAY DIFFRACTION35(chain B and resid 106:117)
36X-RAY DIFFRACTION36(chain B and resid 118:125)
37X-RAY DIFFRACTION37(chain B and resid 126:133)
38X-RAY DIFFRACTION38(chain B and resid 134:143)
39X-RAY DIFFRACTION39(chain B and resid 144:150)
40X-RAY DIFFRACTION40(chain B and resid 151:156)
41X-RAY DIFFRACTION41(chain C and resid 2:15)
42X-RAY DIFFRACTION42(chain C and resid 16:21)
43X-RAY DIFFRACTION43(chain C and resid 22:31)
44X-RAY DIFFRACTION44(chain C and resid 32:37)
45X-RAY DIFFRACTION45(chain C and resid 38:46)
46X-RAY DIFFRACTION46(chain C and resid 47:52)
47X-RAY DIFFRACTION47(chain C and resid 53:57)
48X-RAY DIFFRACTION48(chain C and resid 58:64)
49X-RAY DIFFRACTION49(chain C and resid 65:75)
50X-RAY DIFFRACTION50(chain C and resid 76:83)
51X-RAY DIFFRACTION51(chain C and resid 84:91)
52X-RAY DIFFRACTION52(chain C and resid 92:98)
53X-RAY DIFFRACTION53(chain C and resid 99:105)
54X-RAY DIFFRACTION54(chain C and resid 106:111)
55X-RAY DIFFRACTION55(chain C and resid 112:120)
56X-RAY DIFFRACTION56(chain C and resid 121:126)
57X-RAY DIFFRACTION57(chain C and resid 127:136)
58X-RAY DIFFRACTION58(chain C and resid 137:143)
59X-RAY DIFFRACTION59(chain C and resid 144:154)
60X-RAY DIFFRACTION60(chain C and resid 155:159)
61X-RAY DIFFRACTION61(chain D and resid 4:8)
62X-RAY DIFFRACTION62(chain D and resid 9:14)
63X-RAY DIFFRACTION63(chain D and resid 15:20)
64X-RAY DIFFRACTION64(chain D and resid 21:27)
65X-RAY DIFFRACTION65(chain D and resid 28:36)
66X-RAY DIFFRACTION66(chain D and resid 37:44)
67X-RAY DIFFRACTION67(chain D and resid 45:51)
68X-RAY DIFFRACTION68(chain D and resid 52:57)
69X-RAY DIFFRACTION69(chain D and resid 58:65)
70X-RAY DIFFRACTION70(chain D and resid 66:72)
71X-RAY DIFFRACTION71(chain D and resid 73:77)
72X-RAY DIFFRACTION72(chain D and resid 78:84)
73X-RAY DIFFRACTION73(chain D and resid 85:90)
74X-RAY DIFFRACTION74(chain D and resid 91:97)
75X-RAY DIFFRACTION75(chain D and resid 98:103)
76X-RAY DIFFRACTION76(chain D and resid 104:115)
77X-RAY DIFFRACTION77(chain D and resid 116:123)
78X-RAY DIFFRACTION78(chain D and resid 124:133)
79X-RAY DIFFRACTION79(chain D and resid 134:147)
80X-RAY DIFFRACTION80(chain D and resid 148:156)

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万見について

-
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://pdbjlc1.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