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- PDB-8fhy: Crystal structure of the SARS-CoV-2 receptor binding domain in co... -

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基本情報

登録情報
データベース: PDB / ID: 8fhy
タイトルCrystal structure of the SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5021
要素
  • (WRAIR-5021 Fab ...) x 2
  • Spike protein S1
キーワードVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / viral protein / immune system / RBD / antibody / nonhuman primate / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...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 / 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 / symbiont-mediated suppression of host innate immune response / 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
MALONATE ION / Spike glycoprotein
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
Macaca mulatta (アカゲザル)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.53 Å
データ登録者Sankhala, R.S. / Jensen, J.L. / Joyce, M.G.
資金援助 米国, 1件
組織認可番号国
Department of Defense (DOD, United States)W81XWH-18-2-0040 米国
引用ジャーナル: Nat Commun / 年: 2024
タイトル: Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques.
著者: Sankhala, R.S. / Lal, K.G. / Jensen, J.L. / Dussupt, V. / Mendez-Rivera, L. / Bai, H. / Wieczorek, L. / Mayer, S.V. / Zemil, M. / Wagner, D.A. / Townsley, S.M. / Hajduczki, A. / Chang, W.C. / ...著者: Sankhala, R.S. / Lal, K.G. / Jensen, J.L. / Dussupt, V. / Mendez-Rivera, L. / Bai, H. / Wieczorek, L. / Mayer, S.V. / Zemil, M. / Wagner, D.A. / Townsley, S.M. / Hajduczki, A. / Chang, W.C. / Chen, W.H. / Donofrio, G.C. / Jian, N. / King, H.A.D. / Lorang, C.G. / Martinez, E.J. / Rees, P.A. / Peterson, C.E. / Schmidt, F. / Hart, T.J. / Duso, D.K. / Kummer, L.W. / Casey, S.P. / Williams, J.K. / Kannan, S. / Slike, B.M. / Smith, L. / Swafford, I. / Thomas, P.V. / Tran, U. / Currier, J.R. / Bolton, D.L. / Davidson, E. / Doranz, B.J. / Hatziioannou, T. / Bieniasz, P.D. / Paquin-Proulx, D. / Reiley, W.W. / Rolland, M. / Sullivan, N.J. / Vasan, S. / Collins, N.D. / Modjarrad, K. / Gromowski, G.D. / Polonis, V.R. / Michael, N.L. / Krebs, S.J. / Joyce, M.G.
履歴
登録2022年12月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年1月17日Provider: repository / タイプ: Initial release

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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
I: Spike protein S1
L: WRAIR-5021 Fab Light chain
H: WRAIR-5021 Fab Heavy chain
A: Spike protein S1
B: WRAIR-5021 Fab Light chain
C: WRAIR-5021 Fab Heavy chain
D: Spike protein S1
E: WRAIR-5021 Fab Light chain
F: WRAIR-5021 Fab Heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)212,44234
ポリマ－209,7429
非ポリマー2,70025
水8,701483
1
I: Spike protein S1
L: WRAIR-5021 Fab Light chain
H: WRAIR-5021 Fab Heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,5969
ポリマ－69,9143
非ポリマー6826
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-26 kcal/mol
Surface area26710 Å2
手法PISA
2
A: Spike protein S1
B: WRAIR-5021 Fab Light chain
C: WRAIR-5021 Fab Heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,78011
ポリマ－69,9143
非ポリマー8668
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-18 kcal/mol
Surface area27430 Å2
手法PISA
3
D: Spike protein S1
E: WRAIR-5021 Fab Light chain
F: WRAIR-5021 Fab Heavy chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)71,06614
ポリマ－69,9143
非ポリマー1,15211
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-20 kcal/mol
Surface area26730 Å2
手法PISA
単位格子
Length a, b, c (Å)118.919, 84.127, 119.859
Angle α, β, γ (deg.)90.00, 113.68, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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抗体 , 2種, 6分子 LBEHCF

#2: 抗体 WRAIR-5021 Fab Light chain


分子量: 23356.881 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Macaca mulatta (アカゲザル) / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)
#3: 抗体 WRAIR-5021 Fab Heavy chain


分子量: 23483.328 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Macaca mulatta (アカゲザル) / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト)

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タンパク質 / 糖 , 2種, 6分子 IAD

#1: タンパク質 Spike protein S1


分子量: 23073.766 Da / 分子数: 3 / 断片: receptor binding domain / 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 / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0DTC2
#5: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 3 / 由来タイプ: 組換発現 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 3種, 505分子

#4: 化合物...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 21 / 由来タイプ: 合成 / 式: C3H8O3
#6: 化合物 ChemComp-MLI / MALONATE ION / マロナ-ト


分子量: 102.046 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H2O4
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 483 / 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N

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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: 2.66 Å3/Da / 溶媒含有率: 53.74 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350

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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: 24-ID-E / 波長: 0.9792 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年3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: 0.9792 Å / 相対比: 1
反射解像度: 2.53→109.8 Å / Num. obs: 71266 / % possible obs: 97.8 % / 冗長度: 6.6 % / CC1/2: 0.996 / Net I/σ(I): 11.4
反射 シェル解像度: 2.53→2.58 Å / Num. unique obs: 3598 / CC1/2: 0.625

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
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 / 解像度: 2.53→99.94 Å / SU ML: 0.37 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 27.61 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2562 3875 2.8 %
Rwork0.1953 --
obs0.197 71225 97.02 %
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
精密化ステップサイクル: LAST / 解像度: 2.53→99.94 Å
タンパク質核酸リガンド溶媒全体
原子数14499 0 175 483 15157
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00315019
X-RAY DIFFRACTIONf_angle_d0.55420415
X-RAY DIFFRACTIONf_dihedral_angle_d5.572105
X-RAY DIFFRACTIONf_chiral_restr0.0452264
X-RAY DIFFRACTIONf_plane_restr0.0042616
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.560.3498830.3293087X-RAY DIFFRACTION61
2.56-2.590.3671360.30174270X-RAY DIFFRACTION87
2.59-2.620.35031330.29024557X-RAY DIFFRACTION92
2.62-2.660.32421320.27694749X-RAY DIFFRACTION95
2.66-2.70.32351460.26914898X-RAY DIFFRACTION99
2.7-2.740.33231370.25554878X-RAY DIFFRACTION99
2.74-2.780.26581390.2484944X-RAY DIFFRACTION99
2.78-2.830.31311360.24114923X-RAY DIFFRACTION100
2.83-2.880.29521450.23644935X-RAY DIFFRACTION99
2.88-2.930.33861440.23774919X-RAY DIFFRACTION99
2.93-2.980.29531460.2324911X-RAY DIFFRACTION99
2.98-3.040.28251450.22574932X-RAY DIFFRACTION99
3.04-3.110.28681420.22464884X-RAY DIFFRACTION99
3.11-3.180.30131480.22114920X-RAY DIFFRACTION99
3.18-3.260.32451430.21824900X-RAY DIFFRACTION99
3.26-3.350.27391420.20284885X-RAY DIFFRACTION99
3.35-3.450.31561300.20194913X-RAY DIFFRACTION99
3.45-3.560.25191500.19384896X-RAY DIFFRACTION99
3.56-3.690.24731480.19114938X-RAY DIFFRACTION100
3.69-3.840.24671390.17534982X-RAY DIFFRACTION100
3.84-4.010.25191440.17384876X-RAY DIFFRACTION99
4.01-4.220.24161350.16054908X-RAY DIFFRACTION99
4.22-4.490.1821370.14574876X-RAY DIFFRACTION99
4.49-4.830.21371440.13944938X-RAY DIFFRACTION99
4.83-5.320.1951410.15284842X-RAY DIFFRACTION98
5.32-6.090.1931370.1854952X-RAY DIFFRACTION100
6.09-7.670.26881410.2184936X-RAY DIFFRACTION100
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)
10.77980.0560.2422.2532-0.51484.2618-0.0246-0.71970.22270.427-0.286-0.2407-0.00080.51990.40170.3914-0.08390.01050.8166-0.05990.3801-19.74-16.23724.742
22.71540.9622-0.02464.3471-2.52745.16870.0212-0.4975-0.4479-0.02750.04880.15060.11130.23220.00840.35380.03170.07030.5923-0.00910.3929-26.951-23.41722.517
32.0614-0.53910.16321.5878-1.03372.8123-0.01840.02780.1091-0.0101-0.001-0.0155-0.09830.18290.03490.3013-0.03610.03540.3891-0.01190.3854-28.653-14.3075.205
45.7435-1.77572.0183.7778-2.886.23110.56950.2726-0.7657-0.3377-0.61160.10410.84220.7360.0510.41810.00340.00740.66870.04030.437-18.652-25.09124.457
55.37712.1852-0.88711.27660.29673.334-0.42540.7982-1.3263-0.19860.335-0.16010.6302-0.4313-0.14620.44290.07930.01820.3832-0.05630.6315-48.91-29.552-14.958
63.96770.74670.54990.04720.22910.93530.1064-0.2015-0.58610.00540.00620.02950.0178-0.0101-0.17510.3933-0.0240.01240.38730.08540.4494-54.453-22.493-11.127
74.8692-2.07075.51075.3995-1.34656.44920.51820.66430.5441-0.422-0.7476-0.4421.74930.3149-0.27770.4642-0.03420.08260.5310.03990.5402-72.995-25.427-21.846
83.5160.59051.0833.7238-0.11411.77920.03030.1929-0.1113-0.1102-0.05050.16250.0637-0.3006-0.03470.3297-0.04740.12320.5371-0.02050.3638-78.977-20.192-22.344
92.7836-0.43252.1050.6715-0.39221.7536-0.08160.0140.4096-0.02540.04180.0519-0.2618-0.23180.05160.4070.01840.06380.45520.04650.3931-46.197-3.064-9.852
106.475-1.65252.07251.0148-1.10141.9879-0.22120.47450.7495-0.22880.0842-0.2873-0.31590.24030.33680.3866-0.04670.03150.45250.14270.4762-42.2040.824-15.557
112.7178-0.91530.96720.86790.42192.1305-0.08760.0863-0.0130.45230.17620.1928-0.29040.1312-0.04160.3459-0.02960.01540.52310.09920.3484-52.019-5.749-10.897
122.7614-1.50881.46081.5747-1.63967.90991.2368-0.4219-0.42610.2559-0.4602-0.23450.61190.4312-0.84950.5045-0.0032-0.02130.4876-0.08030.5084-87.035-16.127-11.356
136.07940.92030.47653.21282.05034.12840.252-0.68010.35650.2898-0.34220.4091-0.58620.0629-0.0770.50470.01740.05390.38790.01980.3663-75.649-7.854-9.048
143.49910.659-0.20433.1613-0.18441.78650.1274-0.47360.07010.3709-0.15410.17860.0021-0.1441-0.01990.3167-0.0290.03780.35960.00640.307-78.977-9.363-7.757
153.1574-1.9974-1.73291.86481.0194.694-0.04870.20840.3217-0.3905-0.2802-0.1648-0.4849-0.3811-0.11930.4716-0.06250.09740.52270.05110.48718.854-20.806-75.083
162.7205-1.9566-1.80033.26073.11383.90610.22310.2573-0.1937-0.5589-0.16830.0529-0.0962-0.13450.01510.39780.0701-0.01290.4472-0.00060.27641.826-24.484-72.793
170.1633-0.25320.09273.33213.67924.96330.0466-0.2436-0.4153-0.11130.4194-0.50770.24250.5626-0.37140.4270.0170.02190.6323-0.06740.453913-33.418-68.018
183.5937-0.3544-0.10423.78892.01831.0623-0.017-0.4404-0.21370.31490.134-0.3096-0.05510.0667-0.10490.3491-0.0749-0.01270.4408-0.00970.38390.526-25.503-57.581
194.3071-1.5036-1.05792.48691.32364.77940.16330.04870.27310.0223-0.1211-0.1321-0.3165-0.1119-0.04510.3784-0.02780.00870.36410.03440.29261.192-19.483-57.995
201.490.0251-2.07232.86242.62115.27690.2810.18770.0931-0.2238-0.0440.0147-0.1483-0.3011-0.17760.33430.0206-0.07340.4270.00640.3479-15.465-16.209-53.223
212.23140.0384-1.31922.3207-0.25543.2369-0.038-0.18260.05930.03350.2431-0.3077-0.26570.529-0.04040.3522-0.03330.05270.3801-0.00240.41157.042-18.612-57.185
224.00242.42412.83932.50871.39342.51430.6088-0.3754-1.61840.4485-0.02930.29850.1724-0.2311-0.65750.47460.03790.09950.62150.06490.60694.991-37.977-79.801
238.9639-5.17055.11043.3697-3.43293.50290.0193-0.741-0.33350.45120.17380.17560.1631-0.5922-0.21240.7535-0.07080.05420.53820.02110.3048-15.579-27.268-24.797
244.9622-3.52443.10883.6265-1.58723.23350.3538-0.6875-0.73160.06530.34120.73130.6435-0.5381-0.1950.6703-0.009-0.05560.32440.01620.4938-9.487-35.575-28.137
252.3021-1.16621.32252.5655-0.27073.68880.09080.2623-0.0933-0.07850.04110.15130.45050.0704-0.1240.4603-0.029-0.00370.3214-0.01810.2489-8.389-27.692-34.527
261.00510.13270.26911.02960.06321.87130.1163-0.0232-0.10370.17050.0404-0.16960.27420.159-0.14270.28660.0230.09580.26120.01010.3164-3.458-21.75-9.059
275.20640.8704-1.18673.27230.07388.1163-0.00830.4571-0.4635-0.0058-0.8054-0.05130.6534-0.89970.13340.35060.06830.00270.4452-0.01530.3919-7.132-27.488-2.691
281.78360.1379-0.45182.0340.51554.7115-0.04540.0106-0.0382-0.1971-0.1030.232-0.2605-0.10690.00250.32950.02-0.02470.32690.02010.2961-3.921-20.069-0.58
292.53930.5546-1.42825.83232.81366.3013-0.173-0.26380.03570.5743-0.15190.63970.73110.0371-0.02010.43360.0761-0.00210.40810.04420.3097-4.114-26.8058.536
302.05310.42010.10522.08721.40074.1636-0.1304-0.07260.1903-0.00540.072-0.0154-0.17540.04940.02970.43930.0133-0.02870.3265-0.01140.3687-8.631-5.056-33.279
311.00371.04081.68091.65380.8464.1581-0.06490.07810.2219-0.08020.1194-0.0391-0.21840.00660.03070.41750.03920.02140.3753-0.00840.3577-6.333-4.284-28.591
326.1743-1.0808-0.51771.3932.38694.4154-0.3585-0.5613-0.24410.08170.3401-0.561.01130.245-0.2230.55320.08410.0450.57680.01850.52258.987-20.936.619
337.1728-5.16381.11098.2015-2.54515.14830.1073-0.12630.1150.4010.0878-0.1682-0.19210.2557-0.08490.35790.00430.04920.2724-0.08460.31366.048-14.391-0.993
347.7691-2.83881.60756.8584-1.75986.9020.55110.83560.3454-0.2178-0.5217-0.55720.37710.2452-0.19770.3921-0.18580.19790.4162-0.07420.278610.149-10.489-9.203
354.3169-1.67560.3432.881-0.35982.30080.2766-0.03540.194-0.2386-0.2648-0.2788-0.07220.3702-0.03260.4519-0.04380.03770.3778-0.00610.336810.543-14.412-2.549
367.6591.75380.2530.74330.05411.0260.48660.3797-0.055-0.1153-0.64710.3537-0.2021-0.364-0.06580.42040.04460.02840.7913-0.09420.6061-91.512-11.117-46.786
374.18741.45012.34192.59391.031.32210.2437-0.2332-0.05130.1798-0.30510.31990.3766-0.36550.01960.3587-0.0697-0.02650.5802-0.03810.4708-90.807-17.786-48.215
384.32420.5602-1.85383.3361-0.84241.17190.2396-0.1229-0.3064-0.0504-0.15430.5938-0.1382-0.03970.10570.7134-0.198-0.14320.6568-0.01210.6004-93.216-28.268-51.157
392.06780.30461.01524.0768-0.05143.01-0.002-0.2324-0.5647-0.20630.103-0.08960.7397-0.4519-0.13710.4154-0.05730.01880.54650.00750.3861-78.004-20.327-49.814
401.65990.20340.38461.3225-0.28732.867-0.2083-0.18770.02060.49390.1279-0.0794-0.23150.0059-0.01220.4102-0.04390.0860.5767-0.05530.5276-68.877-9.419-47.054
414.16320.5832-1.571.0994-1.00142.0605-0.0582-0.1806-0.35040.35780.1371-0.02850.1422-0.0008-0.04510.437-0.08130.00720.44220.07610.4599-66.007-18.019-36.222
429.9417-2.19454.76382.1332-1.69292.7609-0.084-0.25421.7523-0.0205-0.3228-0.5625-0.21060.28760.38160.3951-0.07880.07520.4231-0.07060.5544-57.536-9.694-37.854
430.85180.3560.96763.6838-2.75375.462-0.06610.02060.43-0.830.0573-0.37830.1158-0.6294-0.19690.54670.00990.05090.6866-0.08350.4769-70.781-8.205-59.1
441.81141.7951-0.75942.8388-0.41094.85020.090.2302-0.0015-0.06170.17910.05620.5061-1.1479-0.17820.4773-0.153-0.13090.78830.05140.6685-84.689-18.85-49.363
450.26990.4342-0.99254.05271.12675.89120.3745-2.1593-1.0126-0.492-0.0255-0.35580.3208-1.0145-0.36250.5932-0.1934-0.07861.22020.2960.7486-99.519-28.361-39.697
460.3264-0.8707-0.94522.482.83243.2669-0.0707-0.04520.2808-0.06210.4183-0.4155-0.17961.2019-0.64140.47190.0707-0.07360.54340.02330.4737-39.829-28.564-51.664
472.4841-0.0737-0.6143.4323.09075.29970.0388-0.0594-0.23150.2167-0.10950.08480.5189-0.09040.03490.3342-0.0167-0.00890.27910.01950.4158-51.072-28.087-53.608
481.7644-1.0323-0.86730.98321.06411.0566-0.18570.08560.0226-0.0610.04830.06420.1117-0.03620.03820.40310.0232-0.0330.3361-0.03030.3926-41.766-26.898-57.307
494.6204-0.3677-0.79752.0584-0.64272.23390.2767-0.0625-0.0197-0.0825-0.18020.08380.06230.0149-0.09930.3991-0.0221-0.05040.3417-0.03410.2624-21.323-22.421-74.942
503.3321.059-0.73612.91380.45591.8230.3680.19530.16260.0418-0.09940.08790.09110.1986-0.13090.35190.0597-0.04250.4108-0.00090.346-25.82-21.517-74.945
518.22294.6701-1.42027.3648-2.27982.9133-0.25660.2562-0.3189-0.7746-0.0047-0.50770.30020.11560.29210.42070.04630.03640.4736-0.03720.351-16.16-29.388-77.652
524.15110.5692-1.34181.8906-0.26753.57560.0521-0.12850.4356-0.01480.1614-0.1608-0.0504-0.0411-0.2210.2842-0.00230.02460.2169-0.02630.4177-47.825-4.864-52.864
532.7537-0.0739-2.95990.98580.46143.28960.3357-0.10710.3630.0385-0.04060.1647-0.2846-0.0821-0.20490.3037-0.02130.02920.2789-0.02440.4663-42.934-4.66-54.508
548.75545.49282.18033.56212.16975.9979-0.30691.2657-2.2176-0.88020.3875-0.92390.36510.3331-0.62380.69490.05180.00330.6475-0.19790.927-23.889-21.999-86.958
557.61491.40841.71523.74681.27214.6202-0.31120.21210.1919-1.04680.18940.5343-0.3643-0.15950.15470.451-0.0043-0.04270.34390.1580.4073-32.36-12.059-80.243
563.3256-0.1555-1.452.8891-1.05783.1186-0.20860.15950.3168-0.4625-0.02770.3002-0.1536-0.28840.14480.4278-0.0222-0.05260.28690.02990.4098-32.551-15.116-82.134
572.64491.71240.78582.0685-0.53193.96980.05310.90330.2448-1.1308-0.34550.1644-0.7093-0.10480.29980.6675-0.075-0.00180.64330.16590.4466-27.398-10.462-89.63
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN I AND RESID 334:370 )I334 - 370
2X-RAY DIFFRACTION2( CHAIN I AND RESID 371:409 )I371 - 409
3X-RAY DIFFRACTION3( CHAIN I AND RESID 410:506 )I410 - 506
4X-RAY DIFFRACTION4( CHAIN I AND RESID 507:529 )I507 - 529
5X-RAY DIFFRACTION5( CHAIN L AND RESID 1:25 )L1 - 25
6X-RAY DIFFRACTION6( CHAIN L AND RESID 26:139 )L26 - 139
7X-RAY DIFFRACTION7( CHAIN L AND RESID 140:150 )L140 - 150
8X-RAY DIFFRACTION8( CHAIN L AND RESID 151:213 )L151 - 213
9X-RAY DIFFRACTION9( CHAIN H AND RESID 1:53 )H1 - 53
10X-RAY DIFFRACTION10( CHAIN H AND RESID 54:92 )H54 - 92
11X-RAY DIFFRACTION11( CHAIN H AND RESID 93:123 )H93 - 123
12X-RAY DIFFRACTION12( CHAIN H AND RESID 124:138 )H124 - 138
13X-RAY DIFFRACTION13( CHAIN H AND RESID 139:161 )H139 - 161
14X-RAY DIFFRACTION14( CHAIN H AND RESID 162:213 )H162 - 213
15X-RAY DIFFRACTION15( CHAIN A AND RESID 331:349 )A331 - 349
16X-RAY DIFFRACTION16( CHAIN A AND RESID 350:364 )A350 - 364
17X-RAY DIFFRACTION17( CHAIN A AND RESID 365:393 )A365 - 393
18X-RAY DIFFRACTION18( CHAIN A AND RESID 394:421 )A394 - 421
19X-RAY DIFFRACTION19( CHAIN A AND RESID 422:459 )A422 - 459
20X-RAY DIFFRACTION20( CHAIN A AND RESID 460:494 )A460 - 494
21X-RAY DIFFRACTION21( CHAIN A AND RESID 495:516 )A495 - 516
22X-RAY DIFFRACTION22( CHAIN A AND RESID 517:529 )A517 - 529
23X-RAY DIFFRACTION23( CHAIN B AND RESID 1:13 )B1 - 13
24X-RAY DIFFRACTION24( CHAIN B AND RESID 14:25 )B14 - 25
25X-RAY DIFFRACTION25( CHAIN B AND RESID 26:90 )B26 - 90
26X-RAY DIFFRACTION26( CHAIN B AND RESID 91:139 )B91 - 139
27X-RAY DIFFRACTION27( CHAIN B AND RESID 140:150 )B140 - 150
28X-RAY DIFFRACTION28( CHAIN B AND RESID 151:188 )B151 - 188
29X-RAY DIFFRACTION29( CHAIN B AND RESID 189:214 )B189 - 214
30X-RAY DIFFRACTION30( CHAIN C AND RESID 1:68 )C1 - 68
31X-RAY DIFFRACTION31( CHAIN C AND RESID 69:123 )C69 - 123
32X-RAY DIFFRACTION32( CHAIN C AND RESID 124:138 )C124 - 138
33X-RAY DIFFRACTION33( CHAIN C AND RESID 139:149 )C139 - 149
34X-RAY DIFFRACTION34( CHAIN C AND RESID 150:161 )C150 - 161
35X-RAY DIFFRACTION35( CHAIN C AND RESID 162:214 )C162 - 214
36X-RAY DIFFRACTION36( CHAIN D AND RESID 333:349 )D333 - 349
37X-RAY DIFFRACTION37( CHAIN D AND RESID 350:375 )D350 - 375
38X-RAY DIFFRACTION38( CHAIN D AND RESID 376:393 )D376 - 393
39X-RAY DIFFRACTION39( CHAIN D AND RESID 394:442 )D394 - 442
40X-RAY DIFFRACTION40( CHAIN D AND RESID 443:459 )D443 - 459
41X-RAY DIFFRACTION41( CHAIN D AND RESID 460:479 )D460 - 479
42X-RAY DIFFRACTION42( CHAIN D AND RESID 480:494 )D480 - 494
43X-RAY DIFFRACTION43( CHAIN D AND RESID 495:506 )D495 - 506
44X-RAY DIFFRACTION44( CHAIN D AND RESID 507:516 )D507 - 516
45X-RAY DIFFRACTION45( CHAIN D AND RESID 517:529 )D517 - 529
46X-RAY DIFFRACTION46( CHAIN E AND RESID 1:13 )E1 - 13
47X-RAY DIFFRACTION47( CHAIN E AND RESID 14:90 )E14 - 90
48X-RAY DIFFRACTION48( CHAIN E AND RESID 91:113 )E91 - 113
49X-RAY DIFFRACTION49( CHAIN E AND RESID 114:163 )E114 - 163
50X-RAY DIFFRACTION50( CHAIN E AND RESID 164:188 )E164 - 188
51X-RAY DIFFRACTION51( CHAIN E AND RESID 189:214 )E189 - 214
52X-RAY DIFFRACTION52( CHAIN F AND RESID 1:61 )F1 - 61
53X-RAY DIFFRACTION53( CHAIN F AND RESID 62:123 )F62 - 123
54X-RAY DIFFRACTION54( CHAIN F AND RESID 124:138 )F124 - 138
55X-RAY DIFFRACTION55( CHAIN F AND RESID 139:161 )F139 - 161
56X-RAY DIFFRACTION56( CHAIN F AND RESID 162:207 )F162 - 207
57X-RAY DIFFRACTION57( CHAIN F AND RESID 208:215 )F208 - 215

+
万見について

-
お知らせ

-
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

+
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