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- PDB-8sit: Crystal structure of SARS-CoV-2 spike receptor-binding domain in ... -

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基本情報

登録情報
データベース: PDB / ID: 8sit
タイトルCrystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC84.24 Fab
要素
  • CC84.24 fab heavy chain
  • CC84.24 fab light chain
  • Spike protein S1
キーワードIMMUNE SYSTEM / bnAb / SARS-CoV-2 / broadly neutralizing antibody / spike / RBD
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 / membrane fusion / Attachment and Entry / 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: 2.91 Å
データ登録者Liu, H. / Wilson, I.A.
資金援助 米国, 1件
組織認可番号国
Bill & Melinda Gates FoundationINV-004923 米国
引用ジャーナル: Biorxiv / 年: 2023
タイトル: Broadly neutralizing antibodies targeting a conserved silent face of spike RBD resist extreme SARS-CoV-2 antigenic drift
著者: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R. / Torres, J. / He, W. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / Avillion, G. ...著者: Song, G. / Yuan, M. / Liu, H. / Capozzola, T. / Lin, R. / Torres, J. / He, W. / Musharrafieh, R. / Dueker, K. / Zhou, P. / Callaghan, S. / Mishra, N. / Yong, P. / Anzanello, F. / Avillion, G. / Vo, A. / Li, X. / Makhdoomi, M. / Feng, Z. / Zhu, X. / Peng, L. / Nemazee, D. / Safonova, Y. / Briney, B. / Ward, A. / Burton, D. / Wilson, I. / Andrabi, R.
履歴
登録2023年4月16日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年3月13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
A: Spike protein S1
B: Spike protein S1
C: Spike protein S1
D: Spike protein S1
H: CC84.24 fab heavy chain
L: CC84.24 fab light chain
M: CC84.24 fab heavy chain
N: CC84.24 fab light chain
O: CC84.24 fab heavy chain
P: CC84.24 fab light chain
Q: CC84.24 fab heavy chain
S: CC84.24 fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)282,73314
ポリマ－282,29012
非ポリマー4422
水00
1
A: Spike protein S1
H: CC84.24 fab heavy chain
L: CC84.24 fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,7944
ポリマ－70,5733
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Spike protein S1
M: CC84.24 fab heavy chain
N: CC84.24 fab light chain


分子量 (理論値)分子数
合計 (水以外)70,5733
ポリマ－70,5733
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Spike protein S1
O: CC84.24 fab heavy chain
P: CC84.24 fab light chain


分子量 (理論値)分子数
合計 (水以外)70,5733
ポリマ－70,5733
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Spike protein S1
Q: CC84.24 fab heavy chain
S: CC84.24 fab light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)70,7944
ポリマ－70,5733
非ポリマー2211
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)101.394, 105.980, 247.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質
Spike protein S1


分子量: 23104.867 Da / 分子数: 4 / 断片: Receptor binding domain, UNP residues 333-530 / 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)
発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P0DTC2
#2: 抗体
CC84.24 fab heavy chain


分子量: 24752.703 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: Mus musculus (ハツカネズミ)
#3: 抗体
CC84.24 fab light chain


分子量: 22714.957 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: Mus musculus (ハツカネズミ)
#4: 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: 2 / 由来タイプ: 合成 / 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
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: 2.36 Å3/Da / 溶媒含有率: 47.93 %
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: 20% (w/v) PEG 3000, 0.1 M Sodium citrate pH 5.5

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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: 23-ID-B / 波長: 1.03317 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2021年10月8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: 1.03317 Å / 相対比: 1
反射解像度: 2.9→50 Å / Num. obs: 54891 / % possible obs: 92.5 % / 冗長度: 6.2 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.089 / Rrim(I) all: 0.233 / Χ2: 0.933 / Net I/σ(I): 5.1 / Num. measured all: 341806
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.9-2.953.50.76623620.4210.770.430.8850.68781.3
2.95-33.70.73725630.4830.8070.4050.8470.72386.9
3-3.064.20.71225940.6220.8760.370.8060.76388.6
3.06-3.124.50.68326560.6550.890.3440.7690.74991.3
3.12-3.194.90.61527000.7870.9390.2990.6870.78392.4
3.19-3.275.20.61127510.810.9460.2860.6770.79793.2
3.27-3.355.50.53527720.8480.9580.2430.5910.8195.2
3.35-3.445.50.44327390.8920.9710.2010.4890.83893.8
3.44-3.546.30.42428250.9030.9740.180.4630.84595.2
3.54-3.657.10.38828520.9270.9810.1540.420.90696.6
3.65-3.787.30.3528370.9460.9860.1380.3780.91596.3
3.78-3.947.30.30628190.950.9870.1190.330.96996.1
3.94-4.117.30.26728180.9590.990.1040.2881.01995.3
4.11-4.337.40.22527720.9650.9910.0870.2421.10793.6
4.33-4.67.40.19527840.9710.9930.0760.2111.16792.8
4.6-4.967.10.17526990.9750.9940.070.1891.09191.6
4.96-5.467.10.16827910.9740.9930.0670.1821.03692.8
5.46-6.247.80.16528410.9770.9940.0620.1771.0494
6.24-7.867.50.1428460.9820.9950.0540.1510.99193.3
7.86-5070.10228700.9870.9970.0410.110.7789

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.19.2_4158: ???)精密化
HKL-2000データスケーリング
HKL-2000データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.91→48.7 Å / SU ML: 0.43 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 33.81 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.3091 2275 4.89 %Random selection
Rwork0.2611 ---
obs0.2634 46502 78.53 %-
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
精密化ステップサイクル: LAST / 解像度: 2.91→48.7 Å
タンパク質核酸リガンド溶媒全体
原子数17983 0 28 0 18011
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00618486
X-RAY DIFFRACTIONf_angle_d0.97825344
X-RAY DIFFRACTIONf_dihedral_angle_d16.5242697
X-RAY DIFFRACTIONf_chiral_restr0.072821
X-RAY DIFFRACTIONf_plane_restr0.0123340
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-2.970.3823410.3861990X-RAY DIFFRACTION28
2.97-3.040.4469630.35941327X-RAY DIFFRACTION38
3.04-3.120.3627950.33511741X-RAY DIFFRACTION50
3.12-3.20.3811090.33152136X-RAY DIFFRACTION62
3.2-3.30.38681540.33652492X-RAY DIFFRACTION72
3.3-3.40.37431300.32072762X-RAY DIFFRACTION79
3.4-3.530.32451580.31052987X-RAY DIFFRACTION86
3.53-3.670.31141590.28453355X-RAY DIFFRACTION95
3.67-3.830.31941660.27553341X-RAY DIFFRACTION96
3.83-4.040.32811670.26523346X-RAY DIFFRACTION95
4.04-4.290.30251820.24073284X-RAY DIFFRACTION94
4.29-4.620.28641470.20573282X-RAY DIFFRACTION92
4.62-5.080.27891740.21073172X-RAY DIFFRACTION90
5.08-5.820.26841780.22563317X-RAY DIFFRACTION94
5.82-7.330.28271850.26583376X-RAY DIFFRACTION94
7.33-48.70.29211670.25083319X-RAY DIFFRACTION88
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)
10.42880.5408-0.73961.24520.21323.537-0.0671-1.0291-0.54950.7037-0.17040.35090.26190.47940.34530.4687-0.02540.20340.90870.18850.532911.083-41.27448.754
22.29980.1565-0.78412.35880.26561.0437-0.0898-0.49790.23290.449-0.10960.24330.0080.20690.11210.8281-0.48620.08441.5377-0.19970.45389.408-13.86464.837
31.74460.46490.6991.81071.08631.1122-0.0454-0.9289-0.43760.6129-0.1463-0.2560.34710.1775-0.1820.45510.1408-0.01131.61880.25080.38627.345-41.83649.083
40.4944-0.1212-0.66570.4884-0.39341.6049-0.0069-0.76990.15420.2171-0.2549-0.0055-0.35150.34530.11780.8048-0.18310.02172.3347-0.18980.567320.582-17.59775.927
50.71510.4663-0.04430.30810.02020.40810.00980.0964-0.2779-0.0092-0.23780.51550.0493-0.14430.16220.6438-0.04890.05321.4999-0.98591.6963-32.534-74.419-58.015
61.0465-0.1836-1.18170.06040.1661.3959-0.20350.4308-0.2064-0.7018-0.03740.07620.1638-0.80250.38290.94220.1686-0.00571.7968-0.56450.7492-24.689-61.054-64.713
70.1505-0.44540.1941.9387-0.41410.2886-0.06490.1067-0.1222-0.1088-0.12640.16170.1766-0.1942-0.04680.6630.10160.04711.3461-0.83351.1066-20.783-76.132-62.931
80.2357-0.0480.04770.0667-0.32931.79690.03040.2762-0.373-0.75790.01210.24980.4925-0.2858-0.03130.87270.1403-0.23481.6218-0.90641.278-27.352-73.998-66.412
90.75381.44190.89934.03720.33562.568-0.330.8652-0.6233-0.6497-0.0137-0.29360.19660.43650.33490.92760.1654-0.00812.2726-0.77691.1023-6.423-62.96-77.054
100.362-0.3609-0.42540.67310.48321.6976-0.21230.3454-0.2151-0.42090.0990.0006-0.1193-0.07160.21470.60730.0337-0.09981.372-0.72520.9719-17.243-68.877-61.826
110.23080.0873-0.1520.0391-0.00340.4577-0.23830.3468-0.63950.0029-0.16870.18570.2814-0.20420.32130.70840.14440.27141.1282-0.43132.1169-35.855-79.143-37.436
128.7445-2.415-3.15643.3732-2.5025.45340.01130.7839-0.8659-0.3227-0.33940.55780.4851-1.21620.3850.9420.0916-0.20350.7803-0.35231.5211-32.886-77.605-37.995
130.33050.92780.17782.62740.46450.14190.00470.7219-1.4964-0.4929-0.0105-0.03650.0626-0.185-0.05950.76030.11540.09280.8223-0.47941.2967-28.288-74.666-36.923
141.4389-0.0632-1.14542.599-0.66091.10860.27720.6446-0.87550.324-0.20120.314-0.1718-0.0607-0.07751.295-0.1313-0.0090.7625-0.41271.0692-32.815-68.587-32.561
150.6403-0.3146-0.23390.77310.27160.6149-0.01410.605-0.4372-0.1902-0.23510.2535-0.0142-0.4586-0.23910.50950.09660.04611.1731-0.78830.7972-4.822-74.292-58.907
163.1483-0.1953-2.54980.19240.43842.5166-0.2424-0.1832-0.6509-0.027-0.1767-0.01790.0613-0.1180.31791.20980.0162-0.10360.83310.10121.0587-19.982-83.532-28.363
175.6730.7871-0.10990.9940.35080.1715-0.00630.2726-0.29990.34160.0331-0.14110.34920.3992-0.00470.92730.1871-0.14590.96850.06461.5688-24.763-86.215-22.215
180.6086-0.13020.41081.1117-0.17050.5748-0.02880.3648-0.2687-0.4825-0.0760.11620.3142-0.0082-0.20420.23640.0092-0.06860.1731-0.17060.128633.453-25.052-13.779
190.4391-0.28880.96420.5580.03893.3404-0.01020.5021-0.0528-0.1714-0.10.00080.0269-0.00590.05420.2124-0.12770.04710.7216-0.0970.20532.214-17.581-21.369
200.2641-0.2287-0.40320.42741.33534.86710.04420.2091-0.1862-0.4559-0.10150.08550.4798-0.24030.10990.48740.02720.04230.3532-0.26870.408119.642-28.239-20.155
211.25010.5541-0.28381.6241-0.33420.0955-0.11520.85280.2316-0.8735-0.05180.24270.1029-0.35540.1990.39790.0284-0.10620.6314-0.07580.220217.829-17.11-20.303
220.9171-0.39210.09060.289-0.0050.77570.1229-0.22510.04170.05460.14420.0614-0.1432-0.04080.1474-0.0078-0.02150.10790.12750.04570.071325.672-22.153-5.495
231.0154-0.5059-0.10531.45260.56091.39750.03820.2487-0.11570.0620.0937-0.13090.17060.09390.00470.1574-0.02050.08780.1624-0.14250.183327.568-22.773-1.417
241.9695-0.3642-0.18571.267-1.07011.10070.1812-0.21360.38110.3356-0.142-0.42030.06850.11340.03330.278-0.0297-0.01360.0464-0.04190.309436.503-12.8216.806
250.9919-0.3232-0.81132.0097-1.8923.10450.1977-0.82130.48360.5287-0.2724-0.6041-0.47850.78480.0440.1856-0.0501-0.03240.4735-0.05130.345140.031-20.31715.455
261.51030.054-0.33352.5773-0.111.75450.02480.3798-0.1895-0.3327-0.02110.15410.0115-0.0944-0.00380.11920.1022-0.03940.1181-0.11130.147226.165-23.232-11.144
271.8595-1.3456-0.2253.51820.28350.99720.14170.97080.1922-0.8169-0.1854-0.2766-0.18820.3442-0.04590.8617-0.0338-0.00440.7895-0.00950.127913.926-49.895-48.058
281.87861.25561.44871.61840.91472.53850.13660.2481-0.3533-0.11350.2687-0.38090.03790.4606-0.28420.883-0.1024-0.19811.101-0.31810.499917.978-59.258-51.325
291.3960.12750.05310.2259-0.05570.01910.2204-0.2030.4619-0.25330.4968-1.0932-0.07630.9139-0.80530.9535-0.18240.07620.978-0.38640.607625.824-51.543-39.021
302.38662.80362.04343.45661.81333.87040.40950.4447-0.7713-0.15060.0303-0.42160.14060.7176-0.410.37640.0882-0.10110.5342-0.21420.355922.989-62.231-38.201
311.6373-0.2637-0.94080.8261-0.00561.47940.29890.2490.0490.08830.0405-0.2229-0.60420.0505-0.21660.6814-0.0894-0.04270.2636-0.13450.22168.807-52.862-36.653
324.91620.3268-0.73221.0557-0.41372.85930.02630.55360.64080.012-0.09780.2297-0.7355-0.16460.06090.84110.0907-0.11130.3982-0.09790.3855-1.043-42.933-39.824
332.4437-2.0286-0.1753.42350.07851.9782-0.19150.4812-0.1934-0.3528-0.17680.6336-0.6459-0.63410.27670.70560.1514-0.06790.5376-0.20940.3801-8.567-54.864-41.876
342.8029-0.1375-3.60692.02540.04814.6490.38541.0830.0931-0.42770.03940.9538-0.5594-1.1442-0.37860.92040.2898-0.20690.89090.04910.5302-15.135-44.974-40.462
352.20921.45531.20330.96660.86251.30120.16690.00120.5814-0.34-0.11460.3969-0.21030.00960.06991.488-0.0847-0.08490.3492-0.04030.66076.722-36.539-32.889
362.54720.5533-0.922.1910.20172.4876-0.03870.4701-0.5251-0.38510.27-0.46460.15920.4628-0.240.78340.0781-0.1150.517-0.21470.372418.148-60.368-44.839
372.14161.0844-0.31350.5528-0.1730.0963-0.34310.0389-0.3044-0.15620.0918-0.21240.03110.15070.14050.29540.00330.02050.32190.16710.221628.423-39.90312.796
381.96871.94920.11742.72781.38852.0367-0.25170.2378-0.4604-0.2805-0.00610.33450.0811-0.12870.22350.2556-0.17930.05220.3129-0.07960.475619.312-44.8689.686
395.97792.60582.98621.57121.45521.72640.1407-0.0944-1.6666-0.0992-0.3271-0.54591.43280.14510.04040.8620.04790.34710.40580.08370.89428.516-52.82220.756
404.3197-1.58331.92381.6298-0.31724.0666-0.22950.1268-0.88890.045-0.25810.06560.970.03130.40120.53750.08520.32380.38530.07160.483617.614-51.21722.28
413.0679-0.5166-1.64992.24520.40451.9966-0.029-0.6428-0.36840.15560.0047-0.16190.03380.2941-0.04790.1684-0.0631-0.02220.25630.00290.181325.102-36.26224.872
420.75210.26970.07280.86460.47640.73780.0034-0.10340.004-0.09780.1782-0.2259-0.06070.3232-0.08970.1984-0.24730.05740.4854-0.11660.173633.144-24.61222.216
432.7530.8624-0.77610.5408-0.37143.16720.0881-0.21160.69360.0787-0.03750.0519-0.44750.24170.20710.2651-0.0422-0.20320.2371-0.01770.482620.706-18.82121.497
441.70241.25270.43441.90810.10091.6993-0.0065-0.28340.81030.2322-0.082-0.1152-0.38140.14240.15150.2509-0.2203-0.03890.3642-0.06280.484630.056-11.14522.922
450.9125-0.1626-1.55311.3069-0.21412.83420.0986-0.6201-0.26090.1587-0.0449-0.3250.07660.90740.10470.21510.05690.0170.37010.12060.209433.691-36.69524.38
462.76851.01250.08882.64633.58365.54290.03770.0214-1.2308-0.19080.0840.54640.1795-0.0581-0.17220.2648-0.0884-0.10590.5063-0.14550.809110.05-50.57611.49
470.25080.2173-0.21660.5706-0.43011.56240.1630.5799-0.0709-0.8473-0.0941-0.1017-0.10170.2037-0.04831.08140.36040.06431.8079-0.12810.4063-2.13-48.084-77.086
482.68441.62632.48332.23360.21083.6415-0.17250.2634-0.0064-0.31930.00450.1601-0.0646-0.22360.07730.7940.4021-0.16841.5654-0.33920.5169-10.686-50.455-64.713
492.4952-1.06961.78051.3488-1.72344.0994-0.19090.19690.05050.3624-0.2559-0.223-0.12750.50910.37941.04770.3725-0.05691.8301-0.01830.4786.398-49.948-70.849
501.95080.09780.58431.04420.00290.50310.0150.8680.2074-0.0892-0.2243-0.1341-0.5974-0.43470.3061.365-0.0136-0.07541.16770.21020.4639-2.492-41.439-58.75
516.75911.6117-1.90673.3523-1.17137.45220.30880.25550.81980.17690.12070.7353-1.2166-0.2496-0.44781.22950.34690.16520.62450.1550.5481-11.321-34.403-46.248
520.40160.11370.29171.3212-0.30710.3324-0.0191.04570.01-0.0734-0.2494-0.0542-0.8706-0.36220.26710.91610.2455-0.05741.40080.1050.5443-1.778-43.73-63.204
532.1038-0.2791-1.04291.55690.69351.38280.30830.72080.1311-0.139-0.24640.1914-0.2162-0.33730.02190.22830.1143-0.03540.2299-0.0440.19731.941-5.065-0.515
542.51560.4073-0.83592.544-2.20323.55080.0105-0.51250.22480.6289-0.4891-0.6076-0.47650.49060.09490.56050.1714-0.06620.2249-0.19140.6011.218-0.31829.827
550.75670.37260.13591.09230.44160.63360.1040.0703-0.27050.1736-0.18610.1520.06-0.19140.01060.0958-0.054-0.10510.0098-0.2350.18841.08-24.5576.044
562.49591.48041.24775.9322.7063.1582-0.0138-1.04110.04040.63770.04910.31990.0651-0.0369-0.05320.3958-0.02640.02430.79890.11050.334-7.913-8.98539.194
571.8941-0.1758-0.76590.29040.16820.34390.1668-1.1079-0.160.8018-0.42220.28750.2209-0.52320.30461.30550.1159-0.01330.9989-0.16640.5092-7.7-16.08344.491
580.21670.5129-0.1251.2406-0.02011.57710.00470.0861-0.2424-0.10880.01930.20050.3156-0.01260.00710.26320.0551-0.040.0821-0.03870.66044.373-73.377-14.138
596.5793-2.5351.29697.3623-1.56943.24970.37110.8447-0.9097-1.0812-0.3120.21321.08380.5265-0.08810.42930.13650.00810.2386-0.03020.586115.978-73.368-17.647
600.4366-0.372-0.20550.74670.00640.1695-0.00560.1003-0.4187-0.0366-0.1203-0.0074-0.0663-0.01510.08580.38060.2093-0.20750.0967-0.10910.572911.218-71.258-15.611
610.7247-0.05320.09070.8954-0.58450.66080.0075-0.0706-0.14230.0991-0.0999-0.061-0.15070.0607-0.25130.3626-0.0463-0.09710.07130.13320.6249-17.195-70.4362.496
622.2536-0.93810.27192.20050.34961.10250.08840.027-0.75740.0153-0.31810.15530.03450.02940.12760.2284-0.0355-0.05870.1450.02190.7191-19.413-69.415-0.44
630.83040.329-0.15182.61870.86592.09790.1764-0.23390.34440.19840.1073-0.0207-0.48370.2517-0.14640.50520.00390.06970.1072-0.0780.394912.353-52.953-11.774
640.02110.03150.02740.0659-0.04520.4320.08860.118-0.04430.33370.01350.13850.0092-0.1193-0.08120.2517-0.08620.06650.20020.01670.64810.675-47.6121.14
650.97420.23170.00772.0273-0.27040.750.1316-0.2255-0.1520.43410.0105-0.0620.2578-0.16940.00690.4921-0.16690.05480.24510.32180.5087-16.791-60.70414.119
660.7542-0.129-1.04211.1171-0.59162.5934-0.2083-0.6675-0.31390.38270.00260.27250.52030.0610.13570.4165-0.22420.20890.77030.20940.48784.707-40.62547.681
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN O AND RESID 82:118 )O82 - 118
2X-RAY DIFFRACTION2( CHAIN O AND RESID 119:214 )O119 - 214
3X-RAY DIFFRACTION3( CHAIN P AND RESID 3:98 )P3 - 98
4X-RAY DIFFRACTION4( CHAIN P AND RESID 99:209 )P99 - 209
5X-RAY DIFFRACTION5( CHAIN Q AND RESID 2:19 )Q2 - 19
6X-RAY DIFFRACTION6( CHAIN Q AND RESID 20:32 )Q20 - 32
7X-RAY DIFFRACTION7( CHAIN Q AND RESID 33:50 )Q33 - 50
8X-RAY DIFFRACTION8( CHAIN Q AND RESID 51:95 )Q51 - 95
9X-RAY DIFFRACTION9( CHAIN Q AND RESID 96:100 )Q96 - 100
10X-RAY DIFFRACTION10( CHAIN Q AND RESID 101:109 )Q101 - 109
11X-RAY DIFFRACTION11( CHAIN Q AND RESID 110:137 )Q110 - 137
12X-RAY DIFFRACTION12( CHAIN Q AND RESID 138:150 )Q138 - 150
13X-RAY DIFFRACTION13( CHAIN Q AND RESID 151:177 )Q151 - 177
14X-RAY DIFFRACTION14( CHAIN Q AND RESID 178:213 )Q178 - 213
15X-RAY DIFFRACTION15( CHAIN S AND RESID 2:106 )S2 - 106
16X-RAY DIFFRACTION16( CHAIN S AND RESID 107:171 )S107 - 171
17X-RAY DIFFRACTION17( CHAIN S AND RESID 172:209 )S172 - 209
18X-RAY DIFFRACTION18( CHAIN A AND RESID 334:353 )A334 - 353
19X-RAY DIFFRACTION19( CHAIN A AND RESID 354:364 )A354 - 364
20X-RAY DIFFRACTION20( CHAIN A AND RESID 365:375 )A365 - 375
21X-RAY DIFFRACTION21( CHAIN A AND RESID 376:393 )A376 - 393
22X-RAY DIFFRACTION22( CHAIN A AND RESID 394:410 )A394 - 410
23X-RAY DIFFRACTION23( CHAIN A AND RESID 411:459 )A411 - 459
24X-RAY DIFFRACTION24( CHAIN A AND RESID 460:479 )A460 - 479
25X-RAY DIFFRACTION25( CHAIN A AND RESID 480:494 )A480 - 494
26X-RAY DIFFRACTION26( CHAIN A AND RESID 495:528 )A495 - 528
27X-RAY DIFFRACTION27( CHAIN B AND RESID 334:353 )B334 - 353
28X-RAY DIFFRACTION28( CHAIN B AND RESID 354:364 )B354 - 364
29X-RAY DIFFRACTION29( CHAIN B AND RESID 365:375 )B365 - 375
30X-RAY DIFFRACTION30( CHAIN B AND RESID 376:393 )B376 - 393
31X-RAY DIFFRACTION31( CHAIN B AND RESID 394:442 )B394 - 442
32X-RAY DIFFRACTION32( CHAIN B AND RESID 443:459 )B443 - 459
33X-RAY DIFFRACTION33( CHAIN B AND RESID 460:479 )B460 - 479
34X-RAY DIFFRACTION34( CHAIN B AND RESID 480:494 )B480 - 494
35X-RAY DIFFRACTION35( CHAIN B AND RESID 495:506 )B495 - 506
36X-RAY DIFFRACTION36( CHAIN B AND RESID 507:528 )B507 - 528
37X-RAY DIFFRACTION37( CHAIN C AND RESID 334:353 )C334 - 353
38X-RAY DIFFRACTION38( CHAIN C AND RESID 354:364 )C354 - 364
39X-RAY DIFFRACTION39( CHAIN C AND RESID 365:375 )C365 - 375
40X-RAY DIFFRACTION40( CHAIN C AND RESID 376:393 )C376 - 393
41X-RAY DIFFRACTION41( CHAIN C AND RESID 394:442 )C394 - 442
42X-RAY DIFFRACTION42( CHAIN C AND RESID 443:459 )C443 - 459
43X-RAY DIFFRACTION43( CHAIN C AND RESID 460:479 )C460 - 479
44X-RAY DIFFRACTION44( CHAIN C AND RESID 480:494 )C480 - 494
45X-RAY DIFFRACTION45( CHAIN C AND RESID 495:516 )C495 - 516
46X-RAY DIFFRACTION46( CHAIN C AND RESID 517:528 )C517 - 528
47X-RAY DIFFRACTION47( CHAIN D AND RESID 335:410 )D335 - 410
48X-RAY DIFFRACTION48( CHAIN D AND RESID 411:430 )D411 - 430
49X-RAY DIFFRACTION49( CHAIN D AND RESID 431:442 )D431 - 442
50X-RAY DIFFRACTION50( CHAIN D AND RESID 443:469 )D443 - 469
51X-RAY DIFFRACTION51( CHAIN D AND RESID 470:479 )D470 - 479
52X-RAY DIFFRACTION52( CHAIN D AND RESID 480:525 )D480 - 525
53X-RAY DIFFRACTION53( CHAIN H AND RESID 1:103 )H1 - 103
54X-RAY DIFFRACTION54( CHAIN H AND RESID 104:213 )H104 - 213
55X-RAY DIFFRACTION55( CHAIN L AND RESID 1:114 )L1 - 114
56X-RAY DIFFRACTION56( CHAIN L AND RESID 115:190 )L115 - 190
57X-RAY DIFFRACTION57( CHAIN L AND RESID 191:209 )L191 - 209
58X-RAY DIFFRACTION58( CHAIN M AND RESID 1:44 )M1 - 44
59X-RAY DIFFRACTION59( CHAIN M AND RESID 45:59 )M45 - 59
60X-RAY DIFFRACTION60( CHAIN M AND RESID 60:111 )M60 - 111
61X-RAY DIFFRACTION61( CHAIN M AND RESID 112:157 )M112 - 157
62X-RAY DIFFRACTION62( CHAIN M AND RESID 158:214 )M158 - 214
63X-RAY DIFFRACTION63( CHAIN N AND RESID 2:98 )N2 - 98
64X-RAY DIFFRACTION64( CHAIN N AND RESID 99:114 )N99 - 114
65X-RAY DIFFRACTION65( CHAIN N AND RESID 115:209 )N115 - 209
66X-RAY DIFFRACTION66( CHAIN O AND RESID 1:81 )O1 - 81

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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