[日本語] English
万見
- PDB-8drw: Product structure of SARS-CoV-2 Mpro C145A mutant in complex with... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 8drw
タイトルProduct structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp9-nsp10 (C9) cut site sequence
要素Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
キーワードVIRAL PROTEIN / Viral protease / SARS-CoV-2
機能・相同性
機能・相同性情報


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素（リアーゼ）; P-Oリアーゼ類; - / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素（リアーゼ）; P-Oリアーゼ類; - / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / double membrane vesicle viral factory outer membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / SARS-CoV-2 modulates host translation machinery / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / single-stranded RNA binding / host cell perinuclear region of cytoplasm / regulation of autophagy / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / lipid binding / DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell nucleus / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
類似検索 - 分子機能
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Trypsin-like serine proteases / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / :
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Replicase polyprotein 1ab
類似検索 - 構成要素
生物種Severe acute respiratory syndrome coronavirus 2 (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.67 Å
データ登録者Lee, J. / Kenward, C. / Worrall, L.J. / Vuckovic, M. / Paetzel, M. / Strynadka, N.C.J.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR) カナダ
引用ジャーナル: Nat Commun / 年: 2022
タイトル: X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation.
著者: Lee, J. / Kenward, C. / Worrall, L.J. / Vuckovic, M. / Gentile, F. / Ton, A.T. / Ng, M. / Cherkasov, A. / Strynadka, N.C.J. / Paetzel, M.
履歴
登録2022年7月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年9月21日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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

-
集合体

登録構造単位
A: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
B: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
C: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
D: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
E: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
F: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
G: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
H: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
I: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
J: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
K: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
L: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
M: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
N: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)485,395108
ポリマ－473,81114
非ポリマー11,58494
水3,783210
1
A: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
B: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,87821
ポリマ－67,6872
非ポリマー2,19119
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
D: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,72917
ポリマ－67,6872
非ポリマー2,04215
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
F: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,34716
ポリマ－67,6872
非ポリマー1,66014
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
H: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,45715
ポリマ－67,6872
非ポリマー1,76913
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
5
I: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
J: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,37016
ポリマ－67,6872
非ポリマー1,68214
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
6
K: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
L: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,88512
ポリマ－67,6872
非ポリマー1,19810
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
7
M: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
N: Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,72911
ポリマ－67,6872
非ポリマー1,0429
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)275.644, 217.218, 104.635
Angle α, β, γ (deg.)90.000, 110.980, 90.000
Int Tables number5
Space group name H-MC121

-
要素

-
タンパク質 , 1種, 14分子 ABCDEFGHIJKLMN

#1: タンパク質
Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main ...3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase / nsp9


分子量: 33843.609 Da / 分子数: 14 / 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: rep, 1a-1b / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0DTD1, SARS coronavirus main proteinase

-
非ポリマー , 5種, 304分子

#2: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Na
#3: 化合物...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / ペンタエチレングリコ-ル


分子量: 238.278 Da / 分子数: 22 / 由来タイプ: 合成 / 式: C10H22O6 / コメント: 沈殿剤*YM
#4: 化合物...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル


分子量: 106.120 Da / 分子数: 33 / 由来タイプ: 合成 / 式: C4H10O3
#5: 化合物...
ChemComp-PO4 / PHOSPHATE ION / ホスファ-ト


分子量: 94.971 Da / 分子数: 27 / 由来タイプ: 合成 / 式: PO4
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 210 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかN

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.09 Å3/Da / 溶媒含有率: 60.15 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.1M Na/K phosphate (pH 6.2), 50% PEG200

-
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: 1.033 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年7月22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: 1.033 Å / 相対比: 1
反射解像度: 2.67→67.1 Å / Num. obs: 140056 / % possible obs: 99.4 % / 冗長度: 6.8 % / Biso Wilson estimate: 59.6 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.179 / Net I/σ(I): 7.3
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.67-2.856.92.4364757769400.4620.899.8
15.34-49.676.50.0655848640.99520.796.8

-
解析

ソフトウェア
名称バージョン分類
Aimless0.7.7データスケーリング
PHENIX1.20.1_4487精密化
PDB_EXTRACT3.27データ抽出
PHASER位相決定
autoPROCデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 7JOY

7joy


解像度: 2.67→67.1 Å / SU ML: 0.26 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 28.64 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2392 1997 1.65 %
Rwork0.2046 118782 -
obs0.2052 120779 74.71 %
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 max: 182.34 Å2 / Biso mean: 68.283 Å2 / Biso min: 33.88 Å2
精密化ステップサイクル: final / 解像度: 2.67→67.1 Å
タンパク質核酸リガンド溶媒全体
原子数32826 0 613 210 33649
Biso mean--72.29 55.11 -
残基数----4276
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.740.33260.37881663168915
2.74-2.820.4469480.32542512256022
2.82-2.90.3626550.28573848390334
2.9-2.990.316890.27725288537747
2.99-3.10.27511120.28386634674658
3.1-3.220.29251420.28438744888677
3.22-3.370.34311860.282107081089494
3.37-3.550.29081920.24071130711499100
3.55-3.770.24871930.20371136711560100
3.77-4.060.21871880.1891134311531100
4.06-4.470.21751900.17351135011540100
4.47-5.110.19411940.161112971149199
5.11-6.440.23791880.2038112601144899
6.44-67.10.20091940.18151146111655100
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)
11.93872.14770.33223.80211.51251.29380.016-0.12020.6017-0.3914-0.20350.6556-0.2551-0.23740.20480.250.046-0.09360.2921-0.00870.379312.2672160.228930.4617
27.5517-0.49943.05324.67740.63063.3094-0.2787-0.21840.78370.01750.1169-0.292-0.5129-0.02550.13170.42350.02660.01560.2837-0.03450.680822.5356176.037534.7886
33.31380.2680.29713.13480.90982.69970.0516-0.14540.21480.062-0.04870.1962-0.051-0.0623-0.02760.15640.0271-0.02880.2112-0.05470.242717.9775157.375734.451
44.9162-2.15251.09565.97381.66793.65130.0317-0.2494-0.26760.97090.09-0.37390.66950.0651-0.13480.74340.0328-0.1260.3170.01690.527625.4121126.834737.0991
52.88832.35491.39435.63580.1861.1560.72860.26930.34070.7137-0.4386-0.23530.22290.3897-0.20240.5680.0874-0.04260.376-0.02670.241118.8275131.029629.1001
65.98492.5510.35952.48590.32641.53880.0913-0.33590.020.1206-0.1910.59870.2093-0.42470.11440.27270.0015-0.01230.3803-0.00790.425-8.0275138.535317.6737
73.62030.8046-0.03057.05731.3442.5277-0.0103-0.18230.25310.6564-0.21760.72670.0875-0.73790.17510.29470.0306-0.1260.5396-0.14190.531-13.8244146.394716.3398
84.24920.963-0.09650.2503-0.31553.4712-0.24660.18010.067-0.0401-0.00330.00710.1486-0.20.2170.2352-0.0163-0.01790.15210.00790.28254.5772137.981112.8693
93.11930.91110.22472.65910.17423.391-0.09610.0409-0.1529-0.01230.1287-0.33150.15630.0094-0.02280.28130.0042-0.02210.25370.0360.362129.608142.6685.9591
101.7296-0.60270.37432.83540.18832.33080.05280.24640.585-0.1449-0.0553-0.2643-0.39110.0373-0.00610.3291-0.01680.02310.36660.21380.5138100.582158.596315.1428
116.0224-1.70191.17313.4159-0.82881.38460.17190.2349-0.494-0.52490.17380.2970.303-0.2362-0.33770.5541-0.08630.02390.38220.04820.394296.6864126.30436.6616
127.9979-1.43612.83880.6447-0.32391.1395-0.16510.62050.37520.16220.0148-0.2049-0.04880.19350.15690.3055-0.0577-0.01070.26670.04830.3814116.671139.549531.7976
134.61660.39060.17114.6753-1.22773.80040.10640.1254-0.3710.01-0.271-0.91630.24140.72330.15830.3469-0.0347-0.13010.43940.05320.5304127.695133.682937.8549
142.96140.22221.18462.1835-0.3072.8290.11640.095-0.06120.02210.03930.04550.1947-0.1445-0.13830.2125-0.0227-0.05150.1790.02690.324108.2712132.765734.9431
155.2651-2.48490.19148.0902-0.38553.6696-0.0797-0.0572-0.04830.1892-0.01450.4620.13-0.36420.04430.26510.00080.0340.45940.08350.399881.7088135.665937.0403
163.5088-0.75761.2513.09920.45482.8277-0.0455-0.1461-0.2572-0.04380.27420.22720.2513-0.1837-0.21190.3122-0.00240.00420.4250.09180.387683.6574137.858531.3595
173.0296-0.35860.55821.95530.14881.6401-0.3185-0.19550.81620.3375-0.0403-0.8591-0.65040.6090.29260.6829-0.1985-0.31220.58850.08220.726677.1623178.323232.0621
181.2283-0.66930.19971.2179-0.60172.2698-0.1267-0.08580.19850.2142-0.0396-0.0229-0.51390.2610.16950.4495-0.0607-0.16660.4440.02460.438166.0199166.060233.4964
194.1444-0.12960.94094.8579-0.1972.1331-0.3176-0.34650.76080.08470.1785-0.3546-0.43170.13310.15060.4246-0.0423-0.18490.4580.06090.451569.7824168.355734.0456
203.03331.9338-2.12963.2841-1.12412.90320.0064-1.2497-0.21340.0822-0.4668-0.4767-0.10270.19710.49410.44760.0564-0.17430.60390.10680.434375.8856158.148740.144
213.6769-0.1955-0.55213.2856-0.48833.95180.02540.0744-0.00480.0711-0.19190.23550.13820.23270.18240.29080.06120.02270.45430.01950.342949.2163147.526540.6204
223.8191-3.42180.75313.515-0.98152.03550.11890.41470.8495-0.4515-0.3462-0.34010.22660.59410.23510.33790.08510.04180.4349-0.03650.40847.4516155.286529.8592
234.5009-1.73331.54790.913-0.67661.8778-0.3101-0.19450.1152-0.00140.1750.1957-0.5802-0.0990.1570.4697-0.0176-0.1690.2653-0.01180.420149.3807176.137616.5722
245.09420.9591.91154.661-1.17093.1983-0.3167-0.24140.90390.18980.02670.8412-0.6955-0.47540.29830.56640.124-0.1150.3463-0.02050.446738.0958182.780510.8771
254.18640.62310.51992.6243-0.18024.3445-0.0693-0.26170.1935-0.02670.038-0.1338-0.24820.17130.05360.28890.0082-0.11890.2672-0.00810.290952.1815167.549314.1436
263.67350.16710.8031.5549-0.38471.8407-0.06350.1919-0.2384-0.15380.01120.06610.0750.21370.0570.3742-0.0269-0.0310.32110.00630.213353.108156.390911.0733
274.92912.23140.69834.05942.02295.45280.19620.9225-0.414-0.5878-0.1126-0.22030.47450.0967-0.03430.53880.1740.08720.5252-0.03220.449764.5091144.65855.3376
287.47752.24551.50572.43742.5022.5774-0.1310.07170.05230.0725-0.061-0.12960.25760.07750.23830.40450.06640.0040.46580.12910.33767.9029152.228517.4698
293.1746-0.6201-0.5663.71070.98922.00770.0962-0.26410.11870.4464-0.15850.4721-0.3201-0.33810.08080.5140.0490.09920.3479-0.03790.3339-9.7578110.977134.025
306.08711.80140.52819.00961.70223.21370.0861-0.3484-0.23520.63770.0733-0.97190.53290.7014-0.15970.82140.2012-0.13780.51140.01830.641117.624391.983442.7294
310.84532.63451.05679.11163.02643.0113-0.49220.5391-0.26930.9570.9506-0.7948-0.18860.447-0.3890.61450.09870.01050.4963-0.01740.75911.651389.317432.1935
320.65020.74830.80844.94142.22881.32510.2487-0.20480.02640.5454-0.43480.50750.2665-0.37150.1560.2906-0.01230.13330.29480.02530.355-8.622486.829816.8435
336.884-0.5428-0.69243.77342.18733.27360.3239-0.2114-0.89950.28420.06320.27530.6037-0.3909-0.37270.5723-0.1038-0.06270.30950.09150.6774-8.347468.287210.8443
343.1912-4.0430.1996.95762.1983.48080.3795-0.2024-0.8480.4465-0.30390.51510.0878-0.661-0.03540.3533-0.04330.03870.3199-0.04250.6807-17.180581.688110.7367
352.82840.0904-0.11052.48431.43481.6739-0.06760.091-0.2488-0.07550.0625-0.1352-0.09880.2252-0.00610.2532-0.00340.08040.16010.00390.37981.960587.920312.8969
365.7561.5876-0.593.51050.70783.4611-0.14330.95940.1485-0.84640.7098-0.9072-0.86840.5087-0.52610.7555-0.25270.11880.5141-0.09720.645319.336109.05619.7621
371.232-2.471-0.96577.49561.51931.07230.1098-0.36150.1967-0.31720.1795-0.4909-0.10430.3908-0.18860.513-0.09560.06720.377-0.0460.43412.0793109.287218.8267
384.40553.8123-1.98645.1885-2.37171.8769-0.2916-0.1646-0.7618-0.1745-0.0351-0.57030.3513-0.16960.31690.26060.02330.01410.34350.00160.331672.594443.315229.7474
398.10882.3639-3.99915.07440.57577.4585-0.28960.0447-0.0982-0.12940.08170.21970.4601-1.27570.18580.4476-0.07070.00180.63040.0570.39955.803834.683334.4692
404.55711.0258-0.1412.0604-2.1752.8995-0.2707-0.4733-0.4269-0.05380.0505-0.14180.5246-0.26890.21890.39610.05580.14080.40190.05690.338372.551739.794534.5272
413.01921.83370.22734.0393-0.15772.58760.1087-0.46170.35930.208-0.26370.4612-0.2291-0.3050.13120.27520.05940.03890.4304-0.07620.402367.42253.36235.0388
423.2255-0.4178-0.02767.7902-1.5014.4972-0.0085-0.21771.05290.36720.065-0.9167-0.77140.2538-0.13480.5837-0.02690.06220.4203-0.05760.587980.280476.751441.9107
438.97931.0285-1.42393.31180.53581.43570.5570.01010.3797-0.4388-0.1669-0.0459-0.3634-0.5521-0.34530.53890.04910.06850.45120.02220.318384.833872.487730.7927
444.2072-0.0738-2.04681.61070.32491.3877-0.229-0.373-0.45430.14160.1319-0.26410.11070.19870.08920.30390.044-0.04180.26240.05650.26991.634350.846717.1841
456.93411.6069-1.88943.4134-4.35546.4387-0.12380.15740.10640.3019-0.1528-0.9367-0.35410.70090.21860.34090.0022-0.0040.3663-0.05790.428110.045255.001611.2647
466.80193.6297-2.82316.8656-1.03394.7028-0.1613-0.1334-0.4858-0.1411-0.0539-0.63720.61710.50980.19230.35430.03380.00140.2703-0.03310.281599.176143.510111.4724
474.06640.1309-0.42473.71110.03433.2332-0.04440.16550.1465-0.24520.10310.0716-0.3433-0.1683-0.05530.2120.001-0.02840.16870.03630.226988.703660.962212.8076
483.5715-2.39062.46134.9818-2.38525.12490.2072-0.23150.7291-0.14080.33861.2497-0.4961-1.3893-0.51820.38950.1118-0.05960.58780.08050.781461.546272.31513.6512
495.75261.19531.4415.7653-1.69614.6859-0.00211.11970.7578-0.2680.19880.8222-0.4811-0.4088-0.1630.51420.1339-0.11030.65430.15360.765166.021673.97625.4752
507.1894-0.1648-0.10590.2173-0.62712.89960.11460.25680.07070.11050.0971-0.4244-0.55260.1149-0.14490.47130.0978-0.00650.4977-0.07170.465266.28865.25417.2736
513.727-0.7258-0.9473.2213-0.4421.6128-0.3387-0.3443-0.66450.49130.40010.84510.2747-0.1515-0.05760.62010.11980.12840.37890.08070.747314.258152.758129.9887
526.0570.1319-1.40878.52814.25673.34190.2614-0.016-0.01210.7399-0.59930.95190.2718-0.49290.41850.753-0.00220.21110.85960.05091.1358-3.813558.405834.2855
533.3336-1.0850.23375.1473-0.08962.1528-0.452-0.4534-0.76560.64260.22780.60250.402-0.42480.22970.79370.04290.25920.66370.12170.713310.112549.07436.9526
545.2564-0.06730.25123.06540.53562.4987-0.3608-0.84030.18390.66850.5515-0.17050.25810.3186-0.19160.62540.2310.00620.4917-0.01670.591517.846162.905133.6013
557.66340.6683-2.35317.52772.99642.1035-0.13790.27350.3952-1.38840.3111-0.8689-0.74930.0443-0.40.88210.2441-0.38590.9092-0.27081.161346.092772.003731.3133
562.02251.62-1.31766.61330.11442.0148-0.7804-1.82120.84541.83980.7968-1.5198-0.67561.4692-0.0041.17010.2308-0.38941.4753-0.58771.342938.419679.388143.2353
570.122-0.7345-0.56892.0193-1.16666.18690.4744-0.76950.51811.6838-0.0899-2.4953-0.63431.5049-0.72231.02870.0995-0.33331.9052-0.92781.418447.061968.766439.8902
582.11270.2088-1.16220.0518-0.12160.4486-0.2705-0.73450.13060.16790.28520.1149-0.32890.13460.00850.61320.2553-0.19460.8743-0.0960.679942.46164.717131.3954
592.62180.2983-0.38712.3753-0.04761.183-0.5664-0.2994-0.83521.18630.28140.31920.77330.41130.16130.57780.1840.00660.42740.09540.328834.078742.887219.2929
605.24830.6284-0.74783.01440.58273.4086-0.1769-0.4489-0.83810.69390.2839-0.3790.80440.5406-0.04820.69190.25350.03130.50510.03440.631345.337831.983615.1762
613.3763-1.0779-0.90474.2010.94323.155-0.2433-0.08710.2350.30960.20030.15460.40580.14320.0330.29390.0869-0.01210.3045-0.02280.412434.895149.0114.7636
623.3296-4.00161.83214.8317-2.12431.39470.39460.54331.11250.0358-0.7119-2.23010.03230.54270.3360.38780.10120.03320.588-0.00830.929947.83254.53628.4916
631.8862-0.2224-0.64612.463-1.21136.28030.30450.18250.5834-0.0857-0.1507-0.4059-0.72250.4537-0.16450.323-0.03620.02680.31860.03110.733331.350576.38024.2866
647.1005-0.2706-0.64571.87130.71945.72060.24710.03490.2159-0.4997-0.1326-0.369-0.61610.2415-0.07480.27290.1175-0.04180.24540.03960.825327.237274.70112.0041
653.5739-1.9156-2.13822.71590.23282.31390.1842-0.05510.15320.7847-0.0243-0.7117-0.00040.374-0.15230.35370.0263-0.12050.2979-0.02650.588624.14672.749415.4803
663.3050.1299-0.34211.6589-0.8941.6505-0.11250.120.1002-0.4212-0.119-1.2747-0.36420.56310.2030.5366-0.11150.17380.5007-0.09821.0914129.1632106.405914.9697
673.04-0.58670.69853.7588-1.78362.3576-0.05560.30.228-0.5428-0.0052-0.8371-0.00110.09170.05790.5487-0.10050.13220.2484-0.07490.7128115.787105.662312.7058
682.7301-0.46241.01012.69121.47594.9852-0.06980.3160.38-1.13850.12590.8306-0.4515-0.2028-0.03140.7599-0.1326-0.19070.40230.03240.630393.607392.56734.1404
690.5857-1.60120.76136.012-1.28241.6857-0.0664-0.14230.1963-0.48070.38420.6547-0.1213-0.2028-0.30080.5298-0.06150.04030.414-0.10030.528597.48787.38118.7433
702.0862-0.68470.21331.2985-0.79061.8082-0.065-0.248-0.5912-0.1318-0.005-0.71810.33050.25140.04870.41710.0734-0.02390.3598-0.0851.112121.278675.037231.5219
712.3496-2.2935-1.28052.73431.42183.5716-0.0582-0.2393-0.51750.32790.149-0.58230.3649-0.11180.00330.39850.0820.06250.1268-0.12890.7639111.941385.395829.7956
721.7796-0.3614-0.37436.30550.14220.8683-0.0355-0.2134-0.2930.40760.13510.5096-0.24020.0862-0.08670.41490.00610.03380.30570.03370.5328103.452389.906436.1638
733.67513.1650.07329.6557-0.66120.96730.1502-0.0308-0.00210.9255-0.0990.99270.2051-0.2681-0.02750.53620.0530.04920.3277-0.07140.506298.9335103.701838.209
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )A1 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 70 )A44 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 200 )A71 - 200
4X-RAY DIFFRACTION4chain 'A' and (resid 201 through 273 )A201 - 273
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 306 )A274 - 306
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 69 )B1 - 69
7X-RAY DIFFRACTION7chain 'B' and (resid 70 through 100 )B70 - 100
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 200 )B101 - 200
9X-RAY DIFFRACTION9chain 'B' and (resid 201 through 306 )B201 - 306
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 200 )C1 - 200
11X-RAY DIFFRACTION11chain 'C' and (resid 201 through 306 )C201 - 306
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 43 )D1 - 43
13X-RAY DIFFRACTION13chain 'D' and (resid 44 through 100 )D44 - 100
14X-RAY DIFFRACTION14chain 'D' and (resid 101 through 200 )D101 - 200
15X-RAY DIFFRACTION15chain 'D' and (resid 201 through 257 )D201 - 257
16X-RAY DIFFRACTION16chain 'D' and (resid 258 through 306 )D258 - 306
17X-RAY DIFFRACTION17chain 'E' and (resid 1 through 100 )E1 - 100
18X-RAY DIFFRACTION18chain 'E' and (resid 101 through 139 )E101 - 139
19X-RAY DIFFRACTION19chain 'E' and (resid 140 through 180 )E140 - 180
20X-RAY DIFFRACTION20chain 'E' and (resid 181 through 200 )E181 - 200
21X-RAY DIFFRACTION21chain 'E' and (resid 201 through 274 )E201 - 274
22X-RAY DIFFRACTION22chain 'E' and (resid 275 through 306 )E275 - 306
23X-RAY DIFFRACTION23chain 'F' and (resid 1 through 43 )F1 - 43
24X-RAY DIFFRACTION24chain 'F' and (resid 44 through 99 )F44 - 99
25X-RAY DIFFRACTION25chain 'F' and (resid 100 through 155 )F100 - 155
26X-RAY DIFFRACTION26chain 'F' and (resid 156 through 226 )F156 - 226
27X-RAY DIFFRACTION27chain 'F' and (resid 227 through 274 )F227 - 274
28X-RAY DIFFRACTION28chain 'F' and (resid 275 through 306 )F275 - 306
29X-RAY DIFFRACTION29chain 'G' and (resid 1 through 200 )G1 - 200
30X-RAY DIFFRACTION30chain 'G' and (resid 201 through 272 )G201 - 272
31X-RAY DIFFRACTION31chain 'G' and (resid 273 through 306 )G273 - 306
32X-RAY DIFFRACTION32chain 'H' and (resid 1 through 43 )H1 - 43
33X-RAY DIFFRACTION33chain 'H' and (resid 44 through 70 )H44 - 70
34X-RAY DIFFRACTION34chain 'H' and (resid 71 through 100 )H71 - 100
35X-RAY DIFFRACTION35chain 'H' and (resid 101 through 200 )H101 - 200
36X-RAY DIFFRACTION36chain 'H' and (resid 201 through 273 )H201 - 273
37X-RAY DIFFRACTION37chain 'H' and (resid 274 through 306 )H274 - 306
38X-RAY DIFFRACTION38chain 'I' and (resid 1 through 43 )I1 - 43
39X-RAY DIFFRACTION39chain 'I' and (resid 44 through 70 )I44 - 70
40X-RAY DIFFRACTION40chain 'I' and (resid 71 through 120 )I71 - 120
41X-RAY DIFFRACTION41chain 'I' and (resid 121 through 200 )I121 - 200
42X-RAY DIFFRACTION42chain 'I' and (resid 201 through 273 )I201 - 273
43X-RAY DIFFRACTION43chain 'I' and (resid 274 through 306 )I274 - 306
44X-RAY DIFFRACTION44chain 'J' and (resid 1 through 42 )J1 - 42
45X-RAY DIFFRACTION45chain 'J' and (resid 43 through 70 )J43 - 70
46X-RAY DIFFRACTION46chain 'J' and (resid 71 through 100 )J71 - 100
47X-RAY DIFFRACTION47chain 'J' and (resid 101 through 200 )J101 - 200
48X-RAY DIFFRACTION48chain 'J' and (resid 201 through 226 )J201 - 226
49X-RAY DIFFRACTION49chain 'J' and (resid 227 through 273 )J227 - 273
50X-RAY DIFFRACTION50chain 'J' and (resid 274 through 306 )J274 - 306
51X-RAY DIFFRACTION51chain 'K' and (resid 1 through 43 )K1 - 43
52X-RAY DIFFRACTION52chain 'K' and (resid 44 through 70 )K44 - 70
53X-RAY DIFFRACTION53chain 'K' and (resid 71 through 110 )K71 - 110
54X-RAY DIFFRACTION54chain 'K' and (resid 111 through 200 )K111 - 200
55X-RAY DIFFRACTION55chain 'K' and (resid 201 through 224 )K201 - 224
56X-RAY DIFFRACTION56chain 'K' and (resid 225 through 243 )K225 - 243
57X-RAY DIFFRACTION57chain 'K' and (resid 244 through 268 )K244 - 268
58X-RAY DIFFRACTION58chain 'K' and (resid 269 through 306 )K269 - 306
59X-RAY DIFFRACTION59chain 'L' and (resid 1 through 43 )L1 - 43
60X-RAY DIFFRACTION60chain 'L' and (resid 44 through 91 )L44 - 91
61X-RAY DIFFRACTION61chain 'L' and (resid 92 through 180 )L92 - 180
62X-RAY DIFFRACTION62chain 'L' and (resid 181 through 200 )L181 - 200
63X-RAY DIFFRACTION63chain 'L' and (resid 201 through 243 )L201 - 243
64X-RAY DIFFRACTION64chain 'L' and (resid 244 through 274 )L244 - 274
65X-RAY DIFFRACTION65chain 'L' and (resid 275 through 306 )L275 - 306
66X-RAY DIFFRACTION66chain 'M' and (resid 1 through 120 )M1 - 120
67X-RAY DIFFRACTION67chain 'M' and (resid 121 through 200 )M121 - 200
68X-RAY DIFFRACTION68chain 'M' and (resid 201 through 243 )M201 - 243
69X-RAY DIFFRACTION69chain 'M' and (resid 244 through 306 )M244 - 306
70X-RAY DIFFRACTION70chain 'N' and (resid 1 through 120 )N1 - 120
71X-RAY DIFFRACTION71chain 'N' and (resid 121 through 155 )N121 - 155
72X-RAY DIFFRACTION72chain 'N' and (resid 156 through 226 )N156 - 226
73X-RAY DIFFRACTION73chain 'N' and (resid 227 through 306 )N227 - 306

+
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

-
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

+
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

+
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。

-
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