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- PDB-7x7o: SARS-CoV-2 spike RBD in complex with neutralizing antibody UT28K -

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基本情報

登録情報
データベース: PDB / ID: 7x7o
タイトルSARS-CoV-2 spike RBD in complex with neutralizing antibody UT28K
要素
  • Spike protein S1
  • UT28K Fab, heavy chain
  • UT28K Fab, light chain
キーワードVIRAL PROTEIN / SARS-CoV-2 / spike / antibody
機能・相同性
機能・相同性情報


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / symbiont-mediated suppression of host innate immune response / structural constituent of virion ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / symbiont-mediated suppression of host innate immune response / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
類似検索 - ドメイン・相同性
Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.75 Å
データ登録者Ozawa, T. / Tani, H. / Anraku, Y. / Kita, S. / Igarashi, E. / Saga, Y. / Inasaki, N. / Kawasuji, H. / Yamada, H. / Sasaki, S. ...Ozawa, T. / Tani, H. / Anraku, Y. / Kita, S. / Igarashi, E. / Saga, Y. / Inasaki, N. / Kawasuji, H. / Yamada, H. / Sasaki, S. / Somekawa, M. / Sasaki, J. / Hayakawa, Y. / Yamamoto, Y. / Morinaga, Y. / Kurosawa, N. / Isobe, M. / Fukuhara, H. / Maenaka, K. / Hashiguchi, T. / Kishi, H. / Kitajima, I. / Saito, S. / Niimi, H.
資金援助 日本, 1件
組織認可番号国
Japan Agency for Medical Research and Development (AMED)JP21am0101077 日本
引用ジャーナル: MAbs / 年: 2022
タイトル: Novel super-neutralizing antibody UT28K is capable of protecting against infection from a wide variety of SARS-CoV-2 variants.
著者: Tatsuhiko Ozawa / Hideki Tani / Yuki Anraku / Shunsuke Kita / Emiko Igarashi / Yumiko Saga / Noriko Inasaki / Hitoshi Kawasuji / Hiroshi Yamada / So-Ichiro Sasaki / Mayu Somekawa / Jiei ...著者: Tatsuhiko Ozawa / Hideki Tani / Yuki Anraku / Shunsuke Kita / Emiko Igarashi / Yumiko Saga / Noriko Inasaki / Hitoshi Kawasuji / Hiroshi Yamada / So-Ichiro Sasaki / Mayu Somekawa / Jiei Sasaki / Yoshihiro Hayakawa / Yoshihiro Yamamoto / Yoshitomo Morinaga / Nobuyuki Kurosawa / Masaharu Isobe / Hideo Fukuhara / Katsumi Maenaka / Takao Hashiguchi / Hiroyuki Kishi / Isao Kitajima / Shigeru Saito / Hideki Niimi /
要旨: Many potent neutralizing SARS-CoV-2 antibodies have been developed and used for therapies. However, the effectiveness of many antibodies has been reduced against recently emerging SARS-CoV-2 ...Many potent neutralizing SARS-CoV-2 antibodies have been developed and used for therapies. However, the effectiveness of many antibodies has been reduced against recently emerging SARS-CoV-2 variants, especially the Omicron variant. We identified a highly potent SARS-CoV-2 neutralizing antibody, UT28K, in COVID-19 convalescent individuals who recovered from a severe condition. UT28K showed efficacy in neutralizing SARS-CoV-2 in an assay and prophylactic treatment, and the reactivity to the Omicron strain was reduced. The structural analyses revealed that antibody UT28K Fab and SARS-CoV-2 RBD protein interactions were mainly chain-dominated antigen-antibody interactions. In addition, a mutation analysis suggested that the emergence of a UT28K neutralization-resistant SARS-CoV-2 variant was unlikely, as this variant would likely lose its competitive advantage over circulating SARS-CoV-2. Our data suggest that UT28K offers potent protection against SARS-CoV-2, including newly emerging variants.
履歴
登録2022年3月10日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年5月25日Provider: repository / タイプ: Initial release
改定 1.12023年11月29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: Spike protein S1
B: Spike protein S1
C: Spike protein S1
D: Spike protein S1
E: UT28K Fab, heavy chain
F: UT28K Fab, light chain
G: UT28K Fab, heavy chain
H: UT28K Fab, heavy chain
I: UT28K Fab, light chain
J: UT28K Fab, heavy chain
K: UT28K Fab, light chain
L: UT28K Fab, light chain


分子量 (理論値)分子数
合計 (水以外)310,25212
ポリマ－310,25212
非ポリマー00
水00
1
A: Spike protein S1
G: UT28K Fab, heavy chain
I: UT28K Fab, light chain


分子量 (理論値)分子数
合計 (水以外)77,5633
ポリマ－77,5633
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-18 kcal/mol
Surface area18630 Å2
手法PISA
2
B: Spike protein S1
H: UT28K Fab, heavy chain
L: UT28K Fab, light chain


分子量 (理論値)分子数
合計 (水以外)77,5633
ポリマ－77,5633
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-15 kcal/mol
Surface area18250 Å2
手法PISA
3
C: Spike protein S1
E: UT28K Fab, heavy chain
F: UT28K Fab, light chain


分子量 (理論値)分子数
合計 (水以外)77,5633
ポリマ－77,5633
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-18 kcal/mol
Surface area17960 Å2
手法PISA
4
D: Spike protein S1
J: UT28K Fab, heavy chain
K: UT28K Fab, light chain


分子量 (理論値)分子数
合計 (水以外)77,5633
ポリマ－77,5633
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-19 kcal/mol
Surface area18120 Å2
手法PISA
単位格子
Length a, b, c (Å)138.249, 138.412, 221.107
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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要素

#1: タンパク質
Spike protein S1


分子量: 24145.156 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
遺伝子: S, 2 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#2: 抗体
UT28K Fab, heavy chain


分子量: 27689.121 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)
#3: 抗体
UT28K Fab, light chain


分子量: 25728.674 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Homo sapiens (ヒト)

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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: 3.41 Å3/Da / 溶媒含有率: 63.92 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.1 M Citric acid pH5.0, 1.0 M Lithium chloride, 10% (w/v) PEG 6000

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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: SPring-8 / ビームライン: BL32XU / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2021年10月7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: 3.75→48.91 Å / Num. obs: 42875 / % possible obs: 99.9 % / 冗長度: 3.6 % / Biso Wilson estimate: 66.7 Å2 / CC1/2: 0.921 / Net I/σ(I): 7.1
反射 シェル解像度: 3.75→3.89 Å / Num. unique obs: 16957 / CC1/2: 0.469

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0267精密化
Coot0.9.5モデル構築
PHENIX1.18_3845精密化
XDSVERSION Feb 5, 202データ削減
Aimless0.7.7データスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 7jmp

7jmp


解像度: 3.75→48.14 Å / SU ML: 0.7589 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 36.7428
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.3358 2189 5.11 %
Rwork0.3033 40637 -
obs0.305 42826 99.88 %
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: 133.89 Å2
精密化ステップサイクル: LAST / 解像度: 3.75→48.14 Å
タンパク質核酸リガンド溶媒全体
原子数12279 0 0 0 12279
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.005312576
X-RAY DIFFRACTIONf_angle_d0.836417052
X-RAY DIFFRACTIONf_chiral_restr0.05981811
X-RAY DIFFRACTIONf_plane_restr0.00422207
X-RAY DIFFRACTIONf_dihedral_angle_d16.69784466
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.75-3.830.44641230.37112581X-RAY DIFFRACTION99.93
3.83-3.920.37331420.3582482X-RAY DIFFRACTION99.96
3.92-4.020.46221600.34362557X-RAY DIFFRACTION100
4.02-4.130.35831570.3092472X-RAY DIFFRACTION99.85
4.13-4.250.27861030.31862561X-RAY DIFFRACTION100
4.25-4.390.28141470.29132482X-RAY DIFFRACTION99.89
4.39-4.540.34261290.27762588X-RAY DIFFRACTION100
4.54-4.720.25771250.27682510X-RAY DIFFRACTION100
4.72-4.940.27991430.28362553X-RAY DIFFRACTION100
4.94-5.20.33041200.2832512X-RAY DIFFRACTION100
5.2-5.520.30911060.28422583X-RAY DIFFRACTION99.93
5.52-5.950.32251480.30582552X-RAY DIFFRACTION99.96
5.95-6.550.37021740.29052494X-RAY DIFFRACTION100
6.55-7.490.39221560.31842539X-RAY DIFFRACTION99.96
7.49-9.430.34011360.29422567X-RAY DIFFRACTION100
9.43-48.140.32951200.31412604X-RAY DIFFRACTION98.59
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)
17.746514748044.542023474233.134991846262.665287135761.72863482215.46382406929-2.4331080108-0.669521799134-0.9531128731510.5146471602842.483987312970.4801348363531.47415270006-1.44936480594-0.286373014161.795639042510.513017139453-0.7665222720151.151423008310.02848435843782.490962949398.0878749758-55.296119953346.5391874812
26.290016398153.612945028161.65824781312.944933430961.106214132314.88803281781-0.8857644928860.5871001418320.982960048255-1.58705133966-0.3506433659111.062772134750.224738594106-0.2103196910030.4443798616131.510928246760.3994154444040.1806477287420.7320770661710.1135064584471.7259531193123.2380478353-51.138918140849.8769095429
39.206869084435.07889343938-1.576958424589.51072170145-1.486204232894.49272057762.228286640480.2889581099271.422258034050.267271834873-0.4241417130982.010205072921.38732488427-2.17455838873-1.581818272171.41372840369-0.222415644487-0.3511546498311.558738720650.536851206371.934925628397.04117112846-53.004928752552.9091201567
42.01601046951-5.53717679083-1.768069395635.43370114995-3.528069743067.78160896705-0.206907363563-1.88190633217-0.104008176468-0.496255472163-0.23949100880.01016792903192.45594342481-1.912633482850.6205589539950.7383742143-0.4733279232070.3548131147151.70638276669-0.5581966637642.1771457427312.2661650288-66.228003605656.9717854371
53.68707889607-2.744737413390.8198909791663.26535143751.086968918922.91053978788-1.12039886884-0.0920686074195-2.29439218282.032866190940.1562297649891.243129043010.631385865320.4047853453260.9253158312731.283442930130.1166899849750.08991038292421.0049242761-0.1226376156581.4549149250122.9622208502-58.585075137759.3150215662
62.473179019971.60560753467-3.69663274973.40523819572-0.4794091285888.66269742871.41950200743-0.500409357280.3585763725362.4810778030.002584334605120.8651077504770.970106678139-0.121024736384-1.395347592831.75214565074-0.385527617046-0.1107594788781.49783633937-0.1345421811681.3189721349422.6792487777-57.656142168160.9807535213
74.83918551126-3.02818093365-5.918638325744.448471855161.635559884819.30741826641-0.8923446140020.5160654578390.142419784496-0.08799440536530.723451577595-0.9402137169041.876406916781.049990912090.4201711357621.5965577857-0.477250419635-0.4202029166681.5690495781-0.3150699384441.4734830536933.2068800676-56.357433484543.5823691353
83.251764293084.34264858563-2.186560951445.74963101166-2.499866179077.661808879381.05732251961-1.393365136681.04222230763-0.594815098616-0.7398140751031.30818640409-0.3242245772550.375730731535-0.2851785569880.9418333267270.219700077196-0.06985677188991.11729341763-0.1255818328920.86169871446428.4585230273-47.686269577363.8289889422
96.35892341157.167661308444.97260670168.519442861474.851342348995.5244674757-0.08201780374690.98499842892-0.854160683909-0.3027309170332.08220419403-1.01688519726-0.7281576837940.799482574343-2.001448921341.370145069860.3573585737240.2909868357921.17395404459-0.2686988509281.2305600362141.9500343018-41.532182084663.9294886133
102.772049239182.33768446798-3.865743177892.52998442483-2.872397482595.60843278445-1.72842190257-2.47755333205-0.45747786963.052048294640.837630652026-2.81122655377-1.244401609280.7729761845191.070668593281.324424011950.379294547788-0.4604895920771.47717325806-0.1498712066241.7769267902935.7695699391-62.028906194248.2772152626
114.21232995035-1.053450609422.261581813642.776263821941.922818081793.743420755211.06516971282-0.327399042282-1.451423185761.21515910383-0.6421961455310.2594948965780.0708984662891.44584099151-0.1822706808711.54184900723-0.524796165894-0.06036816976451.241907845070.03605673744641.1559592977817.4354950535-58.137256718454.5125213233
122.000188183213.744069694262.000134148064.20982767952.000167940271.999903959481.683529921850.3089049665250.23521783323-5.86226880067-2.43552780476-0.336691306933-3.45510824496-1.290984337510.557361544371.65429101082-0.2863563750820.9743878572481.44535177032-1.007316695733.075589321792.38534552593-54.632765750564.3175941968
134.605489377753.83324411209-1.474665271943.07964302395-1.231353609281.637876308370.6147596341230.923841881139-1.6218976637-0.00772909851732-0.237479308978-0.682045711352-0.223151641430.332773955241-0.4844617505841.22663068930.1163399235070.1620112835420.786044894343-0.06454196865421.4627189481352.5356282676-19.966712727948.2265556896
144.263800871010.1084694545264.714926381960.2872875432060.2354981448865.2871044746-0.154704984551.77360394273-1.172747520890.682156648312-0.179700505064-1.682173817640.1822881746772.139178232941.776612331031.00832290019-0.7076407966580.9790285068021.183917170320.006521318429732.6952462119761.8913166332-21.409630727553.3366321518
152.45409235568-3.07047568324-4.23521246674.363185463164.475993075358.746238785990.414269768503-0.401049426207-1.45864585162-1.083674305292.25989897415-1.3313919926-1.525355208141.36037400562-2.000651898891.31373864329-0.001484113671950.6497825118171.444575373240.01014954156353.1323052162555.1114119295-8.434171925756.5645309793
164.73652709365-4.987991585410.5791317196785.42763650406-0.52040987482.21065556476-2.633345884290.7290676984922.23563852191.159811630231.25518022822-1.319999803160.164260110863-0.1395567557461.555867967660.9175623383420.114761138899-0.06246838565111.443049899060.03344038412361.7894465705246.652377699-15.350064211156.9872717377
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662.537943935535.063896124684.47367047961.996045893628.972879951417.967874853790.241026156310.400402045328-1.183503739093.56845474373-0.365953303593-2.844163244641.647591824581.224021372630.4208508662711.095706193970.4885690873920.1831336586391.065084163270.3915048646271.1399088820222.8622265724-26.675810317875.7540917142
675.09309835312-2.34024902029-0.04898838766854.17922077419-2.443833277832.07675092666-0.322140249834-0.286862632956-0.5448843771750.642329276024-0.3952006758910.364044639837-0.1108703083460.6978282100270.61777029011.276262438250.368335619120.2619203447371.113310929990.4785788283221.303864768164.61083040688-14.157518440870.326746005
685.78207430274-0.4811561753765.211025658385.39750027856-1.584499673455.014094625581.219383215772.025880280961.238412625910.550322702119-0.263979695529-0.4298892462281.455465515392.38235358084-0.8949544874670.8111441746320.10352259210.2153104046671.98475167975-0.5361453117711.1475917833572.6642100624-35.699340795976.3409539178
698.642218074024.971995386930.03442049096747.862618447021.897194405793.806286574211.035919677790.5296402075050.6423046014251.296482469420.248196435193-0.625334998525-0.666937064230.780945341607-0.9730658211760.8069514710790.1443699132550.136284592841.11786009947-0.5502597373031.3049098532962.6588257935-35.866384062171.5847802266
701.99410611045-7.03007562260.3976192429799.09287107035-0.1556152121720.02351367390961.08878092286-2.2010240346-1.207552660952.655850758611.60448711923-1.35964813684-0.5179106942780.552306824948-0.4188650813381.940829199650.54013517635-0.313332262340.62164238965-0.2859332059351.4902592174263.8203213902-48.158890043179.858051814
715.00201264877-0.08431389586390.230918276334.61417718744-3.241695567247.20667334932-0.428524677154-1.346682641141.40628725084-0.6934941693730.181506494077-1.220911134530.6335388793750.7164014311530.1370758624431.18719324737-0.08099900257310.01179455285491.33260714255-0.5674926664541.1353978210160.0921355971-34.972300749280.1737600911
727.054621988773.812884035692.574412095975.01209513475-1.588947314.644339147911.46072096564-2.275974227661.2435658027-0.670664427141-0.8911151373610.840628123522-1.32780031512-1.64313162919-1.051238988491.129149314580.154158828116-0.02227861335350.83297188441-0.4634309763731.4186459398669.9529924425-40.548808868189.2921706211
736.43332584422-2.149855889795.652887314094.268989239370.2893163709156.08713824084-0.1146639554782.385232667710.500572655049-0.3379136144130.525916611368-1.09011539195-0.4989614263463.50264302413-0.4792458598570.9573434107060.304781070604-0.07119131600571.76727140444-0.4610321929351.13174355966.0764177583-41.455467624470.9802947719
747.275177175235.458358586683.8375477384.853443424493.150889516222.149565850091.84203069485-0.6221778872070.8065133669691.53485774634-0.6585427591281.811592241352.16680573627-1.83346031011-0.5627825811071.62246002629-0.62572244258-0.3317504274161.244766700860.3865064027021.080668826199.6177824849210.864718514914.4097891994
753.12300899767-0.958071390227-2.407483888875.28013407541-1.00241999482.406976880640.6154681955131.32438636068-1.705512328891.180181265550.2503504109390.1555156083363.19432013511-0.1326529148420.1052695782262.20477152388-0.663369828132-0.9871459815150.7577958710530.5035611764911.8918570772718.82426634281.4288947041112.2978679846
764.778724707862.796423788731.873140032994.879552638591.227233590940.7533046057340.3513348176560.717498242255-0.634050697009-1.830014910672.11919760043-0.4460993042991.3763323841-0.507087874545-1.083892763361.75424587352-0.246599368305-0.6565685318251.257252951650.2659597732480.85355332377518.222585979511.23931080974.28866958678
777.55593395124-3.903850032883.548667411993.63465609988-1.059345312843.29394748772-0.4431169198940.829293321050.692967182386-0.9469987657420.52642871270.0904537903550.199633174896-0.0638127646904-0.1028762838991.30299443315-0.354542446823-0.3402836912650.86258618130.3878962639861.1209757842513.95592222887.8994652548712.7927307394
782.00397283109-1.64084178881-5.065109666753.23488786824-3.450540074818.608151838371.09762317810.579671283531-3.655812521410.6173169093130.598665031462-1.426014668785.19629238989-1.01130113091-2.124400502722.75577913967-0.537746559007-0.614015625951.12549553666-0.01720428882761.8251809972234.6033497048-0.8241174959129.6919385007
797.07646269515.52917455525-4.336671854018.74310243743-5.420142782264.60643480847-0.2242234119570.419015297872-2.60809635592-1.464704250920.552300655168-0.7191656268634.228577082450.620586653777-0.5604372335781.620586589660.298395653623-0.7430947970610.980573619021-0.3081670983111.5170626383436.8948281765-5.9937765801925.231873138
802.1822106165-3.91321226453-0.2203388349977.800231161242.38808100865.165048783730.462725005809-0.975589568403-0.2183382763030.6578021317611.539199154490.190009067520.8817889284280.891687267436-1.23723858591.42129151687-0.199700757192-0.6672319057790.676833477397-0.1332965416961.448959190633.52045937257.2002507459315.3662351519
810.658634067456-0.9239120322660.07399109713558.47940084622-4.631558514242.87574038998-0.683807443545-1.23422601155-1.248402516551.117850688821.467398973562.45742177481-1.19699695402-0.371660910386-0.4777035219961.03943836294-0.4346253359370.03893152845291.610660842340.2250995439521.5028149650522.98215739833.243382260324.8208598542
822.799331866444.10315486805-4.204767639738.29668799593-6.164341080627.08718797438-1.08182820548-0.820978081360.1720703812260.8832053495010.20199979156-1.700380745690.934658029575-1.998191125760.76118398921.247580367360.0973029139938-0.465618487741.133406769770.06709967200430.98641152776132.518446679910.35744314328.3260566047
831.657430409532.860726179720.6153820587599.49528463118-4.080744845838.33959045495-0.129267354426-0.0701067988787-1.46538990773-0.9191873760211.71937806279-0.8402886394041.79606706149-0.364787486705-0.9336152951741.523045199150.165847216069-0.7903910735451.2725669503-0.2207311511321.7473640789339.48421932224.1859880640321.7633829805
841.994491919451.865678664621.246004362924.156427034753.640144266893.22791480975-0.0616525220141-2.360465797382.182377048662.838962714690.0699454032514-1.96086930174-0.5184664085234.15937899672-0.1110547950071.05177628352-0.369580007218-0.4324330933921.14851501067-0.02716471355961.3748606565330.3900223665-2.7555224656433.9274472307
859.040160504824.87307702313-0.2745353646288.461010047293.197893812221.9335072926-1.784161739821.07091474162-0.778302963504-0.9752930140170.087959875709-2.0647819055-0.8976718667820.612186722454-0.4493606866292.40877373995-0.616482709056-0.630068514420.6731570712110.02972566835181.3516311198629.30757152991.4714695291917.6549955353
863.38364329501-6.221313694954.963140217372.01944637919-9.083849123967.279220735960.84729929161-0.2037026783770.238720282143-3.09331228023-1.51512422668-0.2829999806622.27209368110.438180030145-0.03902677658362.40134538267-0.696930454104-0.4128037680641.299734700840.1163464858281.1571152195929.59511299631.0236785992814.9726590787
871.787143185691.59612868473-3.047953204957.295152944191.361564075068.10503815182-0.2825240425550.038451852003-1.26229459853-0.0567319861803-0.003777385602190.34601052419-0.416447914888-0.6156741667840.3152121175070.807609043925-0.0494559398493-0.07058230491181.648322588130.4500474728511.27889677054-0.642404057368-38.858727142573.5835365802
888.327809742084.7133567524-3.537928453782.73151153872-1.964728550378.504531679450.9342310641870.5063912978340.4821176674650.711962200786-0.165767490598-0.313691756733-0.536652891141-0.149165628115-0.7921490061151.056495400780.3264716839360.133230592780.9994827351420.2839056789590.9132143358787.02839766864-29.117293927276.7964698784
899.87689469312-1.11598056398-6.194336638225.108665279025.539681377868.41412332423-0.569479168264-1.06617917282-0.793222887840.08328441145890.3342342383260.7818949584060.5207486132910.1956554930640.3843298352830.9580166462810.130195850610.002151751290910.9778027851770.4431106973091.06203739086.25837652271-36.415455947382.756218163
906.4524360733-1.89423240125-3.057361415463.329111815490.2851213920546.09674242178-1.423782125552.29128348142-0.2603769376550.2434088017180.631009369678-0.002351541494551.75436914307-2.58358333232-0.1027311922611.290251043720.2306699000710.03409300223721.685996316010.5270761916081.036902995022.90728418576-31.516384202771.1037128691
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 334 through 342 )AA334 - 3421 - 9
22chain 'A' and (resid 343 through 353 )AA343 - 35310 - 20
33chain 'A' and (resid 354 through 364 )AA354 - 36421 - 30
44chain 'A' and (resid 372 through 393 )AA372 - 39331 - 46
55chain 'A' and (resid 394 through 416 )AA394 - 41647 - 69
66chain 'A' and (resid 417 through 437 )AA417 - 43770 - 87
77chain 'A' and (resid 438 through 451 )AA438 - 45188 - 101
88chain 'A' and (resid 452 through 469 )AA452 - 469102 - 119
99chain 'A' and (resid 470 through 494 )AA470 - 494120 - 144
1010chain 'A' and (resid 495 through 506 )AA495 - 506145 - 156
1111chain 'A' and (resid 507 through 516 )AA507 - 516157 - 166
1212chain 'A' and (resid 517 through 524 )AA517167
1313chain 'B' and (resid 334 through 353 )BB334 - 3531 - 20
1414chain 'B' and (resid 354 through 363 )BB354 - 36321 - 30
1515chain 'B' and (resid 373 through 393 )BB373 - 39331 - 41
1616chain 'B' and (resid 394 through 409 )BB394 - 40942 - 57
1717chain 'B' and (resid 410 through 437 )BB410 - 43758 - 85
1818chain 'B' and (resid 438 through 451 )BB438 - 45186 - 99
1919chain 'B' and (resid 452 through 469 )BB452 - 469100 - 117
2020chain 'B' and (resid 470 through 494 )BB470 - 494118 - 142
2121chain 'B' and (resid 495 through 506 )BB495 - 506143 - 154
2222chain 'B' and (resid 507 through 516 )BB507 - 516155 - 164
2323chain 'B' and (resid 517 through 525 )BB517 - 525165 - 172
2424chain 'C' and (resid 335 through 344 )CC335 - 3441 - 10
2525chain 'C' and (resid 345 through 358 )CC345 - 35811 - 24
2626chain 'C' and (resid 359 through 394 )CC359 - 39425 - 37
2727chain 'C' and (resid 395 through 409 )CC395 - 40938 - 52
2828chain 'C' and (resid 410 through 437 )CC410 - 43753 - 80
2929chain 'C' and (resid 438 through 451 )CC438 - 45181 - 94
3030chain 'C' and (resid 452 through 494 )CC452 - 49495 - 137
3131chain 'C' and (resid 495 through 514 )CC495 - 514138 - 157
3232chain 'D' and (resid 333 through 342 )DD333 - 3421 - 10
3333chain 'D' and (resid 343 through 353 )DD343 - 35311 - 21
3434chain 'D' and (resid 354 through 364 )DD354 - 36422 - 31
3535chain 'D' and (resid 365 through 394 )DD365 - 39432 - 45
3636chain 'D' and (resid 395 through 416 )DD395 - 41646 - 67
3737chain 'D' and (resid 417 through 437 )DD417 - 43768 - 85
3838chain 'D' and (resid 438 through 451 )DD438 - 45186 - 99
3939chain 'D' and (resid 452 through 479 )DD452 - 479100 - 127
4040chain 'D' and (resid 480 through 494 )DD480 - 494128 - 142
4141chain 'D' and (resid 495 through 515 )DD495 - 515143 - 163
4242chain 'E' and (resid 2 through 32 )EE2 - 321 - 31
4343chain 'E' and (resid 33 through 60 )EE33 - 6032 - 59
4444chain 'E' and (resid 61 through 73 )EE61 - 7360 - 72
4545chain 'E' and (resid 74 through 91 )EE74 - 9173 - 90
4646chain 'E' and (resid 92 through 108 )EE92 - 10891 - 107
4747chain 'E' and (resid 109 through 123 )EE109 - 123108 - 122
4848chain 'F' and (resid 1 through 30 )FF1 - 301 - 30
4949chain 'F' and (resid 31 through 39 )FF31 - 3931 - 39
5050chain 'F' and (resid 40 through 49 )FF40 - 4940 - 49
5151chain 'F' and (resid 50 through 70 )FF50 - 7050 - 70
5252chain 'F' and (resid 71 through 85 )FF71 - 8571 - 85
5353chain 'F' and (resid 86 through 107 )FF86 - 10786 - 107
5454chain 'G' and (resid 2 through 12 )GG2 - 121 - 11
5555chain 'G' and (resid 13 through 32 )GG13 - 3212 - 31
5656chain 'G' and (resid 33 through 52 )GG33 - 5232 - 51
5757chain 'G' and (resid 53 through 64 )GG53 - 6452 - 63
5858chain 'G' and (resid 65 through 73 )GG65 - 7364 - 72
5959chain 'G' and (resid 74 through 83 )GG74 - 8373 - 82
6060chain 'G' and (resid 84 through 91 )GG84 - 9183 - 90
6161chain 'G' and (resid 92 through 113 )GG92 - 11391 - 112
6262chain 'G' and (resid 114 through 123 )GG114 - 123113 - 122
6363chain 'H' and (resid 2 through 32 )HH2 - 321 - 31
6464chain 'H' and (resid 33 through 73 )HH33 - 7332 - 72
6565chain 'H' and (resid 74 through 98 )HH74 - 9873 - 97
6666chain 'H' and (resid 99 through 108 )HH99 - 10898 - 107
6767chain 'H' and (resid 109 through 123 )HH109 - 123108 - 122
6868chain 'I' and (resid 1 through 18 )II1 - 181 - 18
6969chain 'I' and (resid 19 through 39 )II19 - 3919 - 39
7070chain 'I' and (resid 40 through 49 )II40 - 4940 - 49
7171chain 'I' and (resid 50 through 76 )II50 - 7650 - 76
7272chain 'I' and (resid 77 through 85 )II77 - 8577 - 85
7373chain 'I' and (resid 86 through 107 )II86 - 10786 - 107
7474chain 'J' and (resid 2 through 32 )JJ2 - 321 - 31
7575chain 'J' and (resid 33 through 44 )JJ33 - 4432 - 43
7676chain 'J' and (resid 45 through 73 )JJ45 - 7344 - 72
7777chain 'J' and (resid 74 through 123 )JJ74 - 12373 - 122
7878chain 'K' and (resid 1 through 7 )KK1 - 71 - 7
7979chain 'K' and (resid 8 through 25 )KK8 - 258 - 25
8080chain 'K' and (resid 26 through 39 )KK26 - 3926 - 39
8181chain 'K' and (resid 40 through 49 )KK40 - 4940 - 49
8282chain 'K' and (resid 50 through 62 )KK50 - 6250 - 62
8383chain 'K' and (resid 63 through 76 )KK63 - 7663 - 76
8484chain 'K' and (resid 77 through 85 )KK77 - 8577 - 85
8585chain 'K' and (resid 86 through 91 )KK86 - 9186 - 91
8686chain 'K' and (resid 92 through 107 )KK92 - 10792 - 107
8787chain 'L' and (resid 1 through 30 )LL1 - 301 - 30
8888chain 'L' and (resid 31 through 49 )LL31 - 4931 - 49
8989chain 'L' and (resid 50 through 85 )LL50 - 8550 - 85
9090chain 'L' and (resid 86 through 107 )LL86 - 10786 - 107

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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://pdbjlvh1.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