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- PDB-8xou: Prohead portal vertex of bacteriophage lambda -

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基本情報

登録情報
データベース: PDB / ID: 8xou
タイトルProhead portal vertex of bacteriophage lambda
要素
  • Major capsid protein
  • Portal protein B
キーワードVIRAL PROTEIN (ウイルスタンパク質) / caudovirales / siphoviridae (サイフォウイルス科) / portal vertex / portal / capsid (カプシド) / connector/neck / tail (尾) / delivery device / B-DNA / phage lambda
機能・相同性
機能・相同性情報


symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral portal complex / T=7 icosahedral viral capsid / virion assembly / カプシド / host cell cytoplasm / structural molecule activity / DNA binding
類似検索 - 分子機能
Phage portal protein, lambda family / Phage portal protein, lambda family / Major capsid protein GpE / Phage major capsid protein E
類似検索 - ドメイン・相同性
Portal protein B / Major capsid protein
類似検索 - 構成要素
生物種Escherichia phage Lambda (λファージ)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.58 Å
データ登録者Wang, J.W. / Gu, Z.W.
資金援助 中国, 2件
組織認可番号国
National Natural Science Foundation of China (NSFC)32371254 中国
National Natural Science Foundation of China (NSFC)32171190 中国
引用ジャーナル: J Virol / 年: 2024
タイトル: Structural morphing in the viral portal vertex of bacteriophage lambda.
著者: Zhiwei Gu / Kexun Wu / Jiawei Wang /
要旨: The portal protein of tailed bacteriophage plays essential roles in various aspects of capsid assembly, motor assembly, genome packaging, connector formation, and infection processes. After DNA ...The portal protein of tailed bacteriophage plays essential roles in various aspects of capsid assembly, motor assembly, genome packaging, connector formation, and infection processes. After DNA packaging is complete, additional proteins are assembled onto the portal to form the connector complex, which is crucial as it bridges the mature head and tail. In this study, we report high-resolution cryo-electron microscopy (cryo-EM) structures of the portal vertex from bacteriophage lambda in both its prohead and mature virion states. Comparison of these structures shows that during head maturation, in addition to capsid expansion, the portal protein undergoes conformational changes to establish interactions with the connector proteins. Additionally, the independently assembled tail undergoes morphological alterations at its proximal end, facilitating its connection to the head-tail joining protein and resulting in the formation of a stable portal-connector-tail complex. The B-DNA molecule spirally glides through the tube, interacting with the nozzle blade region of the middle-ring connector protein. These insights elucidate a mechanism for portal maturation and DNA translocation within the phage lambda system.
IMPORTANCE: The tailed bacteriophages possess a distinct portal vertex that consists of a ring of 12 portal proteins associated with a 5-fold capsid shell. This portal protein is crucial in multiple ...IMPORTANCE: The tailed bacteriophages possess a distinct portal vertex that consists of a ring of 12 portal proteins associated with a 5-fold capsid shell. This portal protein is crucial in multiple stages of virus assembly and infection. Our research focused on examining the structures of the portal vertex in both its preliminary prohead state and the fully mature virion state of bacteriophage lambda. By analyzing these structures, we were able to understand how the portal protein undergoes conformational changes during maturation, the mechanism by which it prevents DNA from escaping, and the process of DNA spirally gliding.
履歴
登録2024年1月2日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02024年4月10日Provider: repository / タイプ: Initial release
改定 1.12024年5月8日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年5月29日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume

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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
B: Portal protein B
b: Portal protein B
B1: Portal protein B
b1: Portal protein B
B2: Portal protein B
b2: Portal protein B
B3: Portal protein B
b3: Portal protein B
B4: Portal protein B
b4: Portal protein B
B5: Portal protein B
b5: Portal protein B
A0: Major capsid protein
G0: Major capsid protein
C0: Major capsid protein
D0: Major capsid protein
E0: Major capsid protein
F0: Major capsid protein
A1: Major capsid protein
G1: Major capsid protein
C1: Major capsid protein
D1: Major capsid protein
E1: Major capsid protein
F1: Major capsid protein
A2: Major capsid protein
G2: Major capsid protein
C2: Major capsid protein
D2: Major capsid protein
E2: Major capsid protein
F2: Major capsid protein
A3: Major capsid protein
G3: Major capsid protein
C3: Major capsid protein
D3: Major capsid protein
E3: Major capsid protein
F3: Major capsid protein
A4: Major capsid protein
G4: Major capsid protein
C4: Major capsid protein
D4: Major capsid protein
E4: Major capsid protein
F4: Major capsid protein


分子量 (理論値)分子数
合計 (水以外)1,861,23042
ポリマ－1,861,23042
非ポリマー00
水0
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: 電子顕微鏡法, not applicable
タイプ名称対称操作数
identity operation1_555x,y,z1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1chain "G2"
d_2ens_1chain "A1"
d_3ens_1chain "A2"
d_4ens_1chain "A3"
d_5ens_1chain "A0"
d_6ens_1chain "C0"
d_7ens_1chain "C1"
d_8ens_1chain "C2"
d_9ens_1chain "C3"
d_10ens_1chain "C4"
d_11ens_1chain "D0"
d_12ens_1chain "D1"
d_13ens_1chain "D2"
d_14ens_1chain "D3"
d_15ens_1chain "D4"
d_16ens_1chain "E0"
d_17ens_1chain "E1"
d_18ens_1chain "E2"
d_19ens_1chain "E3"
d_20ens_1chain "E4"
d_21ens_1chain "F0"
d_22ens_1chain "F1"
d_23ens_1chain "F2"
d_24ens_1chain "F3"
d_25ens_1chain "F4"
d_26ens_1chain "G0"
d_27ens_1chain "G1"
d_28ens_1chain "A4"
d_29ens_1chain "G3"
d_30ens_1chain "G4"
d_1ens_2chain "b4"
d_2ens_2chain "B1"
d_3ens_2chain "B2"
d_4ens_2chain "B"
d_5ens_2chain "B4"
d_6ens_2chain "B5"
d_7ens_2chain "b"
d_8ens_2chain "b1"
d_9ens_2chain "b2"
d_10ens_2chain "b3"
d_11ens_2chain "B3"
d_12ens_2chain "b5"

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1ALAALAALAALAG2Z7 - 3417 - 341
d_2ens_1ALAALAALAALAA1S7 - 3417 - 341
d_3ens_1ALAALAALAALAA2Y7 - 3417 - 341
d_4ens_1ALAALAALAALAA3EA7 - 3417 - 341
d_5ens_1ALAALAALAALAA0M7 - 3417 - 341
d_6ens_1ALAALAALAALAC0O7 - 3417 - 341
d_7ens_1ALAALAALAALAC1U7 - 3417 - 341
d_8ens_1ALAALAALAALAC2AA7 - 3417 - 341
d_9ens_1ALAALAALAALAC3GA7 - 3417 - 341
d_10ens_1ALAALAALAALAC4MA7 - 3417 - 341
d_11ens_1ALAALAALAALAD0P7 - 3417 - 341
d_12ens_1ALAALAALAALAD1V7 - 3417 - 341
d_13ens_1ALAALAALAALAD2BA7 - 3417 - 341
d_14ens_1ALAALAALAALAD3HA7 - 3417 - 341
d_15ens_1ALAALAALAALAD4NA7 - 3417 - 341
d_16ens_1ALAALAALAALAE0Q7 - 3417 - 341
d_17ens_1ALAALAALAALAE1W7 - 3417 - 341
d_18ens_1ALAALAALAALAE2CA7 - 3417 - 341
d_19ens_1ALAALAALAALAE3IA7 - 3417 - 341
d_20ens_1ALAALAALAALAE4OA7 - 3417 - 341
d_21ens_1ALAALAALAALAF0R7 - 3417 - 341
d_22ens_1ALAALAALAALAF1X7 - 3417 - 341
d_23ens_1ALAALAALAALAF2DA7 - 3417 - 341
d_24ens_1ALAALAALAALAF3JA7 - 3417 - 341
d_25ens_1ALAALAALAALAF4PA7 - 3417 - 341
d_26ens_1ALAALAALAALAG0N7 - 3417 - 341
d_27ens_1ALAALAALAALAG1T7 - 3417 - 341
d_28ens_1ALAALAALAALAA4KA7 - 3417 - 341
d_29ens_1ALAALAALAALAG3FA7 - 3417 - 341
d_30ens_1ALAALAALAALAG4LA7 - 3417 - 341
d_1ens_2GLNGLNPROPROb4J34 - 50734 - 507
d_2ens_2GLNGLNPROPROB1C34 - 50734 - 507
d_3ens_2GLNGLNPROPROB2E34 - 50734 - 507
d_4ens_2GLNGLNPROPROBA34 - 50734 - 507
d_5ens_2GLNGLNPROPROB4I34 - 50734 - 507
d_6ens_2GLNGLNPROPROB5K34 - 50734 - 507
d_7ens_2GLNGLNPROPRObB34 - 50734 - 507
d_8ens_2GLNGLNPROPROb1D34 - 50734 - 507
d_9ens_2GLNGLNPROPROb2F34 - 50734 - 507
d_10ens_2GLNGLNPROPROb3H34 - 50734 - 507
d_11ens_2GLNGLNPROPROB3G34 - 50734 - 507
d_12ens_2GLNGLNPROPROb5L34 - 50734 - 507

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.503485874053, 0.683494769309, -0.528523296512), (-0.863867154973, -0.387368861672, 0.321992086186), (0.0153464389301, 0.618692383447, 0.785483431701)191.610244463, 375.960302695, -98.4765435246
2given(0.665922413522, 0.576903836874, -0.473000319417), (-0.745799649402, 0.530254270341, -0.403253384036), (0.0181720147602, 0.621298939147, 0.783362882765)-22.5735705485, 255.321784202, -99.2996125
3given(0.914993463171, -0.328747226076, 0.233906442196), (0.402855200638, 0.71244787889, -0.574565668296), (0.0222407210496, 0.619954257355, 0.784322681754)25.9758680885, 14.3415185732, -99.9406744938
4given(-0.977149374497, -0.156278783961, 0.144069572098), (0.211818116308, -0.772299433018, 0.598904559478), (0.0176687725821, 0.615735761056, 0.787754585535)372.532063875, 209.539255308, -98.6090990648
5given(-0.105215233297, 0.993000483155, 0.0536637227283), (-0.852414776535, -0.0622635411946, -0.519145740792), (-0.512170678023, -0.10036579045, 0.85299935796)30.6405735643, 341.034635561, 104.418542742
6given(0.780420104118, 0.366512920836, 0.50656958056), (-0.36341498098, 0.925169664614, -0.109501795767), (-0.508796631954, -0.0986375716306, 0.85521729214)-39.9906634631, 91.4117404407, 103.499304202
7given(0.589022983197, -0.766185156856, 0.256928454398), (0.629983975904, 0.634486359981, 0.44782502063), (-0.506134483482, -0.101918420377, 0.856411419948)175.589158905, -52.901678217, 103.507727453
8given(-0.414902209885, -0.839744261199, -0.350265230956), (0.754938359689, -0.532599699187, 0.382629891012), (-0.507862411783, -0.105674671565, 0.854931947285)379.456588652, 107.530524784, 104.432266926
9given(-0.84396479813, 0.24749177092, -0.475889948249), (-0.161233730389, -0.963214671451, -0.214991118157), (-0.511592712714, -0.104715424024, 0.852823297213)289.873349373, 350.996096509, 104.994971014
10given(0.562970300365, 0.664255898275, 0.49176065572), (-0.161063247436, 0.671777309703, -0.723031034254), (-0.810631279456, 0.327840430356, 0.485177885927)-34.8710778049, 133.66633399, 104.842210354
11given(0.330705020897, -0.43506092057, 0.837470109644), (0.485749072046, 0.839295648229, 0.244193885814), (-0.809124235306, 0.326044184515, 0.488889723337)136.979512999, -34.9749733526, 104.683382853
12given(-0.356221699028, -0.93408254091, 0.0244112250619), (0.464732632985, -0.154444863352, 0.871877493701), (-0.81063535636, 0.321926375048, 0.489115250292)350.470732735, 76.3494658831, 105.47646622
13given(-0.548503664008, -0.143177895374, -0.82379841032), (-0.195068289812, -0.936132335731, 0.292582658932), (-0.813075699354, 0.321179607501, 0.485542548956)310.565874052, 313.793935161, 106.125241799
14given(0.019589627093, 0.844649718359, -0.534960839488), (-0.581831136878, -0.425498658666, -0.693125832466), (-0.813073658822, 0.324834950011, 0.483108145845)72.4112299379, 349.217407721, 105.733183984
15given(0.515387701521, -0.315974472403, 0.796577460082), (0.625296773235, 0.774280072818, -0.097438771639), (-0.585985889337, 0.548316059975, 0.596632245081)138.52976686, -75.7229628241, 1.38505389944
16given(-0.432851825475, -0.836424982145, 0.336203132683), (0.683464337496, -0.0613122706911, 0.727404498772), (-0.587805917419, 0.544641216496, 0.59820577458)390.158300175, 65.2460762032, 2.35072340983
17given(-0.781189553086, -0.202554524977, -0.590520572512), (-0.200378215588, -0.814501551715, 0.544459174753), (-0.591262592142, 0.543653277987, 0.595692588898)333.84254236, 348.118935122, 3.10377901479
18given(-0.0482398239443, 0.709649057248, -0.702901938348), (-0.804798514808, -0.444411047055, -0.393443988159), (-0.591584541675, 0.546714767317, 0.592562817977)47.4116257882, 381.975830294, 2.60554451273
19given(0.753089304367, 0.639551161129, 0.154372315997), (-0.294502870031, 0.537510636064, -0.790158449719), (-0.588323515756, 0.549596787124, 0.593143163487)-73.2985281558, 120.026505286, 1.54309664288
20given(-0.312977004358, -0.651201454005, 0.691362467194), (0.917757237558, -0.0199875059712, 0.3966385666), (-0.244472999843, 0.758641658431, 0.603900477265)321.222339758, -3.44513423904, -78.7773811165
21given(-0.968471760996, -0.185555532747, -0.166227532077), (-0.0140176618224, -0.62560383568, 0.780014965203), (-0.248728674082, 0.757752588283, 0.603278593719)378.224986095, 261.342559888, -77.8403209617
22given(-0.284854315872, 0.534312342912, -0.795844418804), (-0.925368684758, -0.369898469063, 0.0828729138802), (-0.250101611348, 0.760056210288, 0.599803085357)144.010131438, 397.380434989, -77.913658807
23given(0.793140284607, 0.513566599588, -0.327380263181), (-0.556839359745, 0.393753812488, -0.731360282344), (-0.246694986516, 0.762369518631, 0.598276107403)-57.7443616384, 216.66846899, -78.8956905218
24given(0.775758913702, -0.219120538489, 0.591763717564), (0.582274537752, 0.610009724685, -0.537442553652), (-0.243216920666, 0.761494796701, 0.60080879163)51.778587336, -31.0554834784, -79.4296785283
25given(-0.809009037775, 0.587792824192, -0.0019931451711), (-0.587769326928, -0.808999821794, -0.00681957913892), (-0.00562095377009, -0.00434559156151, 0.999974760038)203.99540379, 402.149055764, 1.67054194233
26given(0.309019256645, 0.951054627651, 0.00148129847242), (-0.95104565867, 0.309022778868, -0.00413246493903), (-0.00438795487415, -0.000131771237817, 0.999990364198)-44.0923533646, 275.180910385, 0.756530033913
27given(-0.100481061296, -0.781880556359, 0.615277459289), (0.994697256976, -0.0925752755016, 0.0448016219662), (0.0219299631949, 0.616516515557, 0.787036506625)270.164575116, -13.9540174256, -99.5142406099
28given(0.309019836325, -0.951045465213, -0.00438906090004), (0.951054441536, 0.309023352452, -0.000129899017634), (0.00147986218511, -0.00413409448999, 0.999990359589)275.338416714, -43.103096881, 0.44689400119
29given(-0.809008923295, -0.587769474002, -0.00562205123884), (0.587792979398, -0.808999707276, -0.00434591731528), (-0.00199384027205, -0.00682048813597, 0.999974752453)401.414469196, 205.438492902, 1.47921460537
30given(-0.866233749962, 0.499586408771, -0.00724641975886), (-0.499527255179, -0.866255662338, -0.00858188795127), (-0.0105646467298, -0.00381413680976, 0.99993691831)229.10615342, 397.273306993, 2.42127965231
31given(-0.865613489083, -0.500596945917, -0.0107696451225), (0.500654335359, -0.865640845565, -0.00334110392227), (-0.00765009829079, -0.0082839741444, 0.999936423863)397.07001864, 229.353957507, 2.65979893816
32given(0.000659860091524, 0.999997810528, -0.00198583070215), (-0.999963745985, 0.000642976330675, -0.00849077720052), (-0.00848948176807, 0.00199136143283, 0.999961980867)-0.243637452439, 335.641692543, 1.08253343028
33given(0.866038702382, -0.499972161246, -0.00219179284802), (0.499975890999, 0.866037607939, 0.00172338459993), (0.00103653071211, -0.0025883613447, 0.999996112987)106.436102572, -61.3258242374, 0.264292967823
34given(0.865744625055, 0.500484733794, 0.00112934847084), (-0.500478714792, 0.865741986983, -0.00344499850986), (-0.00270189355127, 0.002417274072, 0.999993428257)-61.5644384557, 106.564145949, 0.0380619591809
35given(-0.500661551902, 0.865629095071, -0.00492749558685), (-0.865583698153, -0.500685769155, -0.00886690798484), (-0.0101425804529, -0.000174160059568, 0.999948547541)106.379641129, 397.238547252, 1.74542054495
36given(-0.999954256576, -0.000263845247988, -0.00956112656656), (0.000328425138128, -0.999977141046, -0.00675348219967), (-0.00955912613502, -0.00675631338659, 0.999931485321)335.518170838, 335.916095441, 2.74190550275
37given(-0.499272484906, -0.866389285472, -0.00982811452798), (0.866434795038, -0.499289595621, -0.000803524735947), (-0.00421091010656, -0.00891659818826, 0.999951380074)397.012398115, 106.518970924, 2.21463650282
38given(0.500697045378, -0.865604738897, -0.00555920398345), (0.86562239135, 0.500690958301, 0.00253768959118), (0.000586807033895, -0.00608278512655, 0.999981327517)229.223559939, -61.3510645415, 0.941177701407
39given(-0.000128814840256, -0.999964957448, -0.00837062018429), (0.999998753227, -0.000141984130489, 0.00157270011784), (-0.00157383350164, -0.00837040716091, 0.999963729008)335.745656066, 0.239957480368, 1.66777063319
40given(0.499901550875, 0.86608214182, 0.000403798902482), (-0.866068597503, 0.499896240957, -0.00537891218397), (-0.00486043733841, 0.00233920899364, 0.999985452019)-61.5789607979, 229.207299598, 0.444447828918

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要素

#1: タンパク質
Portal protein B / GpB / Minor capsid protein B


分子量: 59529.609 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia phage Lambda (λファージ)
遺伝子: B / 発現宿主: Escherichia phage Lambda (λファージ) / 参照: UniProt: P03710
#2: タンパク質 ...
Major capsid protein / Gene product E / gpE / Major head protein


分子量: 38229.160 Da / 分子数: 30 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia phage Lambda (λファージ)
遺伝子: E / 発現宿主: Escherichia phage Lambda (λファージ) / 参照: UniProt: P03713

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: PARTICLE / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Escherichia phage Lambda / タイプ: VIRUS / Entity ID: all / 由来: NATURAL
由来(天然)生物種: Escherichia phage Lambda (λファージ)
ウイルスについての詳細中空か: YES / エンベロープを持つか: NO / 単離: STRAIN / タイプ: VIRION
緩衝液pH: 7
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結凍結剤: NITROGEN

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELDBright-field microscopy / 最大 デフォーカス（公称値）: 2000 nm / 最小 デフォーカス（公称値）: 1000 nm
撮影電子線照射量: 50 e/Å2
フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k)

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解析

CTF補正タイプ: NONE
3次元再構成解像度: 5.58 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 50921 / 対称性のタイプ: POINT
精密化交差検証法: NONE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
原子変位パラメータBiso mean: 354.63 Å2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.0042126138
ELECTRON MICROSCOPYf_angle_d0.95170706
ELECTRON MICROSCOPYf_chiral_restr0.051618330
ELECTRON MICROSCOPYf_plane_restr0.009222602
ELECTRON MICROSCOPYf_dihedral_angle_d6.944417418
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2ZG2ELECTRON MICROSCOPYNCS constraints3.7268497101E-10
ens_1d_3ZG2ELECTRON MICROSCOPYNCS constraints6.7536465702E-11
ens_1d_4ZG2ELECTRON MICROSCOPYNCS constraints3.37770689455E-13
ens_1d_5ZG2ELECTRON MICROSCOPYNCS constraints2.56285863562E-11
ens_1d_6ZG2ELECTRON MICROSCOPYNCS constraints1.07542587476E-12
ens_1d_7ZG2ELECTRON MICROSCOPYNCS constraints8.86521759109E-11
ens_1d_8ZG2ELECTRON MICROSCOPYNCS constraints1.53718483024E-12
ens_1d_9ZG2ELECTRON MICROSCOPYNCS constraints5.7793781758E-13
ens_1d_10ZG2ELECTRON MICROSCOPYNCS constraints3.23028370234E-13
ens_1d_11ZG2ELECTRON MICROSCOPYNCS constraints3.20943597374E-13
ens_1d_12ZG2ELECTRON MICROSCOPYNCS constraints3.38971022399E-13
ens_1d_13ZG2ELECTRON MICROSCOPYNCS constraints2.95333980263E-10
ens_1d_14ZG2ELECTRON MICROSCOPYNCS constraints6.76239361598E-13
ens_1d_15ZG2ELECTRON MICROSCOPYNCS constraints5.04018332296E-13
ens_1d_16ZG2ELECTRON MICROSCOPYNCS constraints2.30100268447E-11
ens_1d_17ZG2ELECTRON MICROSCOPYNCS constraints1.61625108101E-10
ens_1d_18ZG2ELECTRON MICROSCOPYNCS constraints7.48756422628E-11
ens_1d_19ZG2ELECTRON MICROSCOPYNCS constraints7.93199340951E-13
ens_1d_20ZG2ELECTRON MICROSCOPYNCS constraints4.62303008248E-13
ens_1d_21ZG2ELECTRON MICROSCOPYNCS constraints8.48841434027E-11
ens_1d_22ZG2ELECTRON MICROSCOPYNCS constraints5.92816914564E-13
ens_1d_23ZG2ELECTRON MICROSCOPYNCS constraints6.83252122772E-13
ens_1d_24ZG2ELECTRON MICROSCOPYNCS constraints8.20085928914E-13
ens_1d_25ZG2ELECTRON MICROSCOPYNCS constraints4.16136389111E-11
ens_1d_26ZG2ELECTRON MICROSCOPYNCS constraints2.6577608974E-11
ens_1d_27ZG2ELECTRON MICROSCOPYNCS constraints3.32471027443E-10
ens_1d_28ZG2ELECTRON MICROSCOPYNCS constraints3.44796186641E-12
ens_1d_29ZG2ELECTRON MICROSCOPYNCS constraints5.78853117977E-13
ens_1d_30ZG2ELECTRON MICROSCOPYNCS constraints8.15714255985E-12
ens_2d_2Jb4ELECTRON MICROSCOPYNCS constraints3.45777884273E-11
ens_2d_3Jb4ELECTRON MICROSCOPYNCS constraints3.72947434633E-11
ens_2d_4Jb4ELECTRON MICROSCOPYNCS constraints5.68448489728E-12
ens_2d_5Jb4ELECTRON MICROSCOPYNCS constraints1.55575274643E-11
ens_2d_6Jb4ELECTRON MICROSCOPYNCS constraints2.86423235599E-13
ens_2d_7Jb4ELECTRON MICROSCOPYNCS constraints7.26109788393E-11
ens_2d_8Jb4ELECTRON MICROSCOPYNCS constraints5.76752425835E-12
ens_2d_9Jb4ELECTRON MICROSCOPYNCS constraints7.25448216678E-13
ens_2d_10Jb4ELECTRON MICROSCOPYNCS constraints1.23120159927E-10
ens_2d_11Jb4ELECTRON MICROSCOPYNCS constraints9.69328281573E-13
ens_2d_12Jb4ELECTRON MICROSCOPYNCS constraints4.91435204128E-11

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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