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- PDB-9hls: Structure of A16/G9 (vaccinia virus) in complex with VHH D07, VHH... -

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基本情報

登録情報
データベース: PDB / ID: 9hls
タイトルStructure of A16/G9 (vaccinia virus) in complex with VHH D07, VHH B01 and VHH C05
要素
  • Entry-fusion complex protein OPG094
  • VHH B01
  • VHH C05
  • VHH D07
  • Virion membrane protein OPG143
キーワードVIRAL PROTEIN / poxvirus / viral fusion / vaccinia virus / mpox virus
機能・相同性
機能・相同性情報


membrane fusion involved in viral entry into host cell / DNA-templated transcription termination / helicase activity / hydrolase activity / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / virion membrane / DNA binding / ATP binding / membrane
類似検索 - 分子機能
Pox virus entry-fusion-complex G9/A16 / Pox virus entry-fusion-complex G9/A16
類似検索 - ドメイン・相同性
: / PHOSPHATE ION / Entry-fusion complex protein OPG094 / Virion membrane protein OPG143
類似検索 - 構成要素
生物種Vaccinia virus Western Reserve (ウイルス)
Vicugna pacos (アルパカ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.2 Å
データ登録者Vernuccio, R. / Meola, A. / Guardado-Calvo, P.
資金援助 フランス, 1件
組織認可番号国
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0003 フランス
引用ジャーナル: Cell / 年: 2025
タイトル: Structural basis of poxvirus fusion regulation and anti-A16/G9 antibody-mediated neutralization and protection.
著者: Annalisa Meola / Riccardo Vernuccio / Leandro Battini / Guillermo Albericio / Pilar Delgado / Rebecca Bamford / Laura Pokorny / Manon Broutin / Alejandro Martínez León / Sébastien Gallien ...著者: Annalisa Meola / Riccardo Vernuccio / Leandro Battini / Guillermo Albericio / Pilar Delgado / Rebecca Bamford / Laura Pokorny / Manon Broutin / Alejandro Martínez León / Sébastien Gallien / María Gil / María A Noriega / Florence Guivel-Benhassine / Françoise Porrot / Jeanne Postal / Julian Buchrieser / Mathieu Hubert / Ahmed Haouz / Pierre Lafaye / Mariano Esteban / Jochen S Hub / Matthieu Mahévas / Pascal Chappert / Jason Mercer / Juan Garcia-Arriaza / Olivier Schwartz / Pablo Guardado-Calvo /
要旨: Monkeypox virus (MPXV) is a poxvirus endemic to Central and West Africa with high epidemic potential. Poxviruses enter host cells via a conserved entry-fusion complex (EFC), which mediates viral ...Monkeypox virus (MPXV) is a poxvirus endemic to Central and West Africa with high epidemic potential. Poxviruses enter host cells via a conserved entry-fusion complex (EFC), which mediates viral fusion to the cell membrane. The EFC is a promising therapeutic target, but the absence of structural data has limited the development of fusion-inhibiting treatments. Here, we investigated A16/G9, a subcomplex of the EFC that controls fusion timing. Using cryo-electron microscopy, we showed how A16/G9 interacts with A56/K2, a viral fusion suppressor that prevents superinfection. Immunization with A16/G9 elicited a protective immune response in mice. Using X-ray crystallography, we characterized two neutralizing antibodies and engineered a chimeric antibody that cross-neutralizes several poxviruses more efficiently than 7D11, the most potent antibody targeting the EFC described to date. These findings highlight the potential of A16/G9 as a candidate for subunit vaccines and identify regions of the EFC as targets for antiviral development.
履歴
登録2024年12月5日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年9月3日Provider: repository / タイプ: Initial release
改定 1.12025年9月10日Group: Database references / カテゴリ: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Virion membrane protein OPG143
B: Entry-fusion complex protein OPG094
C: VHH D07
D: VHH B01
J: VHH C05
F: Virion membrane protein OPG143
G: Entry-fusion complex protein OPG094
H: VHH D07
I: VHH B01
E: VHH C05
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)259,53717
ポリマ－259,09610
非ポリマー4417
水1086
1
A: Virion membrane protein OPG143
B: Entry-fusion complex protein OPG094
C: VHH D07
D: VHH B01
E: VHH C05
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)129,6827
ポリマ－129,5485
非ポリマー1342
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
J: VHH C05
F: Virion membrane protein OPG143
G: Entry-fusion complex protein OPG094
H: VHH D07
I: VHH B01
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)129,85510
ポリマ－129,5485
非ポリマー3075
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)150.435, 194.282, 94.866
Angle α, β, γ (deg.)90.000, 91.263, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1chain "A"
d_2ens_1chain "F"
d_1ens_2chain "B"
d_2ens_2chain "G"
d_1ens_3(chain "C" and (resid 3 through 40 or resid 45 through 119))
d_2ens_3chain "H"
d_1ens_4chain "D"
d_2ens_4chain "I"
d_1ens_5chain "E"
d_2ens_5(chain "J" and resid 3 through 122)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALCYSCYSAA5 - 29124 - 310
d_21ens_1VALVALCYSCYSFF5 - 29124 - 310
d_11ens_2VALVALASNASNBB7 - 26824 - 285
d_21ens_2VALVALASNASNGG7 - 26824 - 285
d_11ens_3GLUGLUARGARGCC3 - 403 - 40
d_12ens_3LYSLYSSERSERCC45 - 11945 - 119
d_21ens_3GLUGLUSERSERHH3 - 1193 - 119
d_11ens_4VALVALVALVALDD4 - 1204 - 120
d_21ens_4VALVALVALVALII4 - 1204 - 120
d_11ens_5ASPASPSERSEREJ3 - 1223 - 122
d_21ens_5ASPASPSERSERJE3 - 1223 - 122

NCSアンサンブル:
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixベクター
1given(0.999527080807, 9.2062050342E-5, 0.0307507114915), (-0.000660172751443, -0.99970080415, 0.0244513057542), (0.0307437620436, -0.0244600430442, -0.999227965676)-0.300028873193, 27.3871913077, -1.97578892024
2given(0.999138236426, 5.62681381275E-5, 0.0415064012615), (-0.000330191182701, -0.999956663062, 0.00930392237991), (0.0415051260155, -0.00930960964623, -0.999094918255)-0.209564444947, 27.6990750987, -2.56662197876
3given(0.99757359318, 0.0194307571296, 0.0668533609299), (0.0175357487378, -0.999430883282, 0.0288167843271), (0.067375245502, -0.0275745393455, -0.997346590245)-0.52953252305, 26.8045351211, -3.61381979624
4given(0.98912359383, 0.0299559623672, 0.14400401539), (0.0270451780916, -0.999389249701, 0.0221288482542), (0.14457895584, -0.0179935516704, -0.989329650635)-1.80366595868, 26.7842788013, -5.14937444416
5given(0.998358396782, -0.0197672799237, 0.0537565458192), (-0.0198298880813, -0.999803169015, 0.000631479613251), (0.053733482231, -0.00169642926152, -0.998553871864)-0.158625444702, 28.8577446395, -3.06632479026

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要素

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タンパク質 , 2種, 4分子 AFBG

#1: タンパク質 Virion membrane protein OPG143


分子量: 40941.340 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Vaccinia virus Western Reserve (ウイルス)
遺伝子: OPG143, VACWR136, A16L / 細胞株 (発現宿主): S2 cells
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
参照: UniProt: P16710
#2: タンパク質 Entry-fusion complex protein OPG094 / EFC protein OPG094 / Myristoylated protein G9 / Protein F1


分子量: 37432.238 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Vaccinia virus Western Reserve (ウイルス)
遺伝子: OPG094, VACWR087, G9R / 細胞株 (発現宿主): S2 cells
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
参照: UniProt: P07611

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抗体 , 3種, 6分子 CHDIJE

#3: 抗体 VHH D07


分子量: 16965.787 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#4: 抗体 VHH B01


分子量: 17044.777 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#5: 抗体 VHH C05


分子量: 17163.922 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)

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非ポリマー , 3種, 13分子

#6: 化合物
ChemComp-K / POTASSIUM ION


分子量: 39.098 Da / 分子数: 4 / 由来タイプ: 合成 / 式: K / タイプ: SUBJECT OF INVESTIGATION
#7: 化合物 ChemComp-PO4 / PHOSPHATE ION


分子量: 94.971 Da / 分子数: 3 / 由来タイプ: 合成 / 式: PO4 / タイプ: SUBJECT OF INVESTIGATION
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 6 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
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: 2.68 Å3/Da / 溶媒含有率: 54.18 %
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
詳細: 20% w/v PEG 3350, 0.2 M KH2PO4 (cryoprotected with 33% Ethylene glycol)

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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: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.978565 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2024年5月16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: 0.978565 Å / 相対比: 1
反射解像度: 3.2→39.72 Å / Num. obs: 44399 / % possible obs: 99 % / 冗長度: 5.9 % / Biso Wilson estimate: 66.43 Å2 / CC1/2: 0.971 / Net I/σ(I): 4.2
反射 シェル解像度: 3.2→3.32 Å / Num. unique obs: 4713 / CC1/2: 0.563

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21.2_5419精密化
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.2→39.72 Å / SU ML: 0.4898 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 32.965
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2923 2117 4.78 %
Rwork0.2367 42210 -
obs0.2394 44327 98.87 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 83.6 Å2
精密化ステップサイクル: LAST / 解像度: 3.2→39.72 Å
タンパク質核酸リガンド溶媒全体
原子数14301 0 19 6 14326
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.001714645
X-RAY DIFFRACTIONf_angle_d0.455919812
X-RAY DIFFRACTIONf_chiral_restr0.03972071
X-RAY DIFFRACTIONf_plane_restr0.00412590
X-RAY DIFFRACTIONf_dihedral_angle_d10.14245402
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.469137791732
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.483874738158
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.10892961049
ens_4d_2DDX-RAY DIFFRACTIONTorsion NCS0.66913540799
ens_5d_2JEX-RAY DIFFRACTIONTorsion NCS0.580673361583
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.270.40271570.34532816X-RAY DIFFRACTION99.27
3.27-3.360.35651470.33662802X-RAY DIFFRACTION99.36
3.36-3.450.36521430.31562797X-RAY DIFFRACTION99.22
3.45-3.550.35131300.29342835X-RAY DIFFRACTION99.33
3.55-3.660.38121390.26772838X-RAY DIFFRACTION98.94
3.66-3.790.3481260.27222795X-RAY DIFFRACTION98.28
3.79-3.950.32511280.25292832X-RAY DIFFRACTION99.6
3.95-4.120.27681500.2482813X-RAY DIFFRACTION99.56
4.12-4.340.29661470.22122813X-RAY DIFFRACTION99.46
4.34-4.610.30251470.20532808X-RAY DIFFRACTION99.26
4.61-4.970.25751550.19482826X-RAY DIFFRACTION99.14
4.97-5.470.24251370.20682800X-RAY DIFFRACTION98.39
5.47-6.260.27591470.22922828X-RAY DIFFRACTION99.13
6.26-7.870.2541400.21782820X-RAY DIFFRACTION98.77
7.87-39.720.21351240.1872787X-RAY DIFFRACTION95.44
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)
10.660079110694-0.358541425193-0.8246233884010.4478640989240.701261608841.128153048740.02997025486380.794778844134-0.4851842242341.17773187526-0.53830222668-0.250129649679-0.6378420869730.814528774870.0007703069098761.03544037922-0.296039200551-0.2320367051981.20545393545-0.072085460831.08038787896.221539653356.259959908512.071783446
21.833167640220.8770458957570.4736315497262.479684625551.488816700091.61445652234-0.4024633807080.4862790118710.187306851534-0.04390069871590.1298909063060.0392602793636-0.4618408519590.0567913446039-6.62793321461E-50.802815180334-0.0510629713145-0.08185903302410.7979372184910.0309677110210.75095458852783.914676079448.655014120114.3986864623
30.4788396703191.733633770030.6035113755812.31726281470.6895252739180.144560123074-0.0291085905251-0.0301810055239-0.3281030570110.2219254122310.411375333795-0.09526571162110.100077870930.3695891629939.67808597627E-50.801817096923-0.0748140603376-0.0366103693090.7891988760840.05615048190480.69041705947963.456194321518.242385765210.1932156189
43.208962253712.21712753421-1.427115153812.63481700909-0.6379034024091.67957361853-0.406628162010.216563002074-0.449380674954-0.234168578370.294961225495-0.1953892017110.1286296943880.171081988925-0.0001077145131480.611762823560.02001680283440.05570753705870.8676316040540.02709174279610.69809783946142.140445032-5.9973126282612.3992582931
52.809883418021.10444737908-0.3847116945280.741303797965-0.02884101591890.6838151540530.0648299160917-0.1449102662730.03493338867550.0151662004539-0.15324253369-0.00869115052771-0.08108687633210.206872411168-9.26375487327E-60.700844015672-0.0174118325844-0.03950160284160.8065402858510.0124660388230.67734632758259.871968055934.839852359412.3613052821
61.365954259321.02799971099-0.730623653093.125403142231.637115959571.997002668450.205878269881-0.1605369690960.174555396438-0.0726517242301-0.161720601540.0112934035274-0.265233068318-0.0619816079297-4.89305397884E-50.7006690106050.0242110949669-0.05459112468920.8405312472010.01274314422840.73215893131339.334509112321.274866403316.4977668374
70.717026840687-0.311946907174-0.5841737326860.2174518518450.3039907301150.447906074291-0.861841531583-0.807375638015-0.1300955308740.08877400069880.353073865751-0.551445817616-0.2326735954560.8886205924160.005126587299160.6910784108340.0227368515408-0.1627028484430.822139627180.05483922866670.72241382051741.19606589048.245562222926.7120016163
81.583549940470.788962937596-0.3198020075391.83688484099-0.9422917813180.578466000561-0.0136448199612-0.258669797246-0.1798846218120.1858417485620.0273356593534-0.02633643926360.1002113500080.07251759057090.0001885895060140.612016334544-0.04029257794430.004334700214010.757086697836-0.01432672008460.74146230915225.8569506621-6.8870658155829.2552119478
91.73342197080.3854261849470.7503434839990.2968102841180.4022258440860.5549131130590.23974132824-0.256743761188-0.8527790618920.215196410453-0.0444078588310.172126568473-0.05239369694130.5866617227060.003272029378081.49569673036-0.2300315715390.1745612943211.532267516760.4720301161160.76537476369418.6082958695-33.104902788250.4844474546
100.4024333296890.423542545688-0.2657668857440.483069121443-0.3259029712780.5208288106940.4903338398710.195853956289-0.4712383263580.636083081209-1.381264812990.7355591395820.0535749131985-0.388477352625-0.0003333064906411.360532456570.0917006646179-0.06640134234140.967142971728-0.02039458440621.0495523897220.2465050606-22.550892658151.0061262124
110.4368877101590.468467229778-0.1864386194980.453499535988-0.2027965838490.04900163514890.1069785052370.191671535267-0.2842434774440.0735604440409-0.2287368611330.623263447635-0.1513815842020.4752881903520.0006027059432020.8889712684-0.1427585378210.05964961996441.01802727242-0.02242770691991.0817028273719.6435045604-28.510783867539.9033993822
120.09508817044650.05263178453320.134087802874-0.002922758590590.05787014777980.171640574614-0.193437730586-1.558916590110.3674802384881.45112225281-0.1978780786130.551770455631-0.05824696456710.7189024569440.0006298884119670.957596324839-0.03092844940980.07897849004351.412111970830.1591059276511.3303507945110.2848945558-22.938325061940.326667823
130.3408357591460.3556654279150.4107096334920.835174760270.832022353590.765690795779-0.04894542753250.260273622225-0.145404175770.671772795071-0.2052173051370.262510676271-0.0196154548090.02205826985110.0005985947918580.783537781674-0.042084725321-0.1643457287721.08715839790.09151930499910.80044578054722.5986790651-19.101534792539.0672491032
140.6600011334580.6869622840570.4844926224280.9983583151670.1370667841631.14556887881-0.1792686196840.104475482742-0.7186588150360.614546156491-0.004400589373521.199620807690.1497240378880.1136328676647.88888226483E-51.202113593260.04979142041070.06348161747510.4506869186370.03822489838820.90438738401320.4758592314-20.01532233147.5991126796
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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 5 through 28 )AA5 - 281 - 24
22chain 'A' and (resid 29 through 127 )AA29 - 12725 - 123
33chain 'A' and (resid 128 through 182 )AA128 - 182124 - 178
44chain 'A' and (resid 183 through 291 )AA183 - 291179 - 287
55chain 'B' and (resid 7 through 95 )BB7 - 951 - 89
66chain 'B' and (resid 96 through 143 )BB96 - 14390 - 137
77chain 'B' and (resid 144 through 159 )BB144 - 159138 - 153
88chain 'B' and (resid 160 through 268 )BB160 - 268154 - 262
99chain 'C' and (resid 3 through 12 )CC3 - 121 - 10
1010chain 'C' and (resid 13 through 30 )CC13 - 3011 - 28
1111chain 'C' and (resid 31 through 41 )CC31 - 4129 - 39
1212chain 'C' and (resid 42 through 53 )CC42 - 5340 - 51
1313chain 'C' and (resid 54 through 74 )CC54 - 7452 - 72
1414chain 'C' and (resid 75 through 93 )CC75 - 9373 - 91
1515chain 'C' and (resid 94 through 119 )CC94 - 11992 - 117
1616chain 'D' and (resid 4 through 68 )DD4 - 681 - 65
1717chain 'D' and (resid 69 through 120 )DD69 - 12066 - 117
1818chain 'J' and (resid 3 through 54 )JE3 - 541 - 52
1919chain 'J' and (resid 55 through 68 )JE55 - 6853 - 66
2020chain 'J' and (resid 69 through 92 )JE69 - 9267 - 90
2121chain 'J' and (resid 93 through 103 )JE93 - 10391 - 101
2222chain 'J' and (resid 104 through 123 )JE104 - 123102 - 121
2323chain 'F' and (resid 5 through 28 )FF5 - 281 - 24
2424chain 'F' and (resid 29 through 108 )FF29 - 10825 - 104
2525chain 'F' and (resid 109 through 182 )FF109 - 182105 - 178
2626chain 'F' and (resid 183 through 238 )FF183 - 238179 - 234
2727chain 'F' and (resid 239 through 291 )FF239 - 291235 - 287
2828chain 'G' and (resid 7 through 116 )GG7 - 1161 - 110
2929chain 'G' and (resid 117 through 268 )GG117 - 268111 - 262
3030chain 'H' and (resid 3 through 12 )HH3 - 121 - 10
3131chain 'H' and (resid 13 through 19 )HH13 - 1911 - 17
3232chain 'H' and (resid 20 through 30 )HH20 - 3018 - 28
3333chain 'H' and (resid 31 through 61 )HH31 - 6129 - 55
3434chain 'H' and (resid 62 through 74 )HH62 - 7456 - 68
3535chain 'H' and (resid 75 through 84 )HH75 - 8469 - 78
3636chain 'H' and (resid 85 through 101 )HH85 - 10179 - 95
3737chain 'H' and (resid 102 through 119 )HH102 - 11996 - 113
3838chain 'I' and (resid 4 through 18 )II4 - 181 - 15
3939chain 'I' and (resid 19 through 31 )II19 - 3116 - 28
4040chain 'I' and (resid 32 through 47 )II32 - 4729 - 44
4141chain 'I' and (resid 48 through 61 )II48 - 6145 - 58
4242chain 'I' and (resid 62 through 75 )II62 - 7559 - 72
4343chain 'I' and (resid 76 through 108 )II76 - 10873 - 105
4444chain 'I' and (resid 109 through 120 )II109 - 120106 - 117
4545chain 'E' and (resid 3 through 28 )EJ3 - 281 - 26
4646chain 'E' and (resid 29 through 41 )EJ29 - 4127 - 39
4747chain 'E' and (resid 42 through 47 )EJ42 - 4740 - 45
4848chain 'E' and (resid 48 through 54 )EJ48 - 5446 - 52
4949chain 'E' and (resid 55 through 68 )EJ55 - 6853 - 66
5050chain 'E' and (resid 69 through 78 )EJ69 - 7867 - 76
5151chain 'E' and (resid 79 through 92 )EJ79 - 9277 - 90
5252chain 'E' and (resid 93 through 103 )EJ93 - 10391 - 101
5353chain 'E' and (resid 104 through 112 )EJ104 - 112102 - 110
5454chain 'E' and (resid 113 through 122 )EJ113 - 122111 - 120

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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