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- PDB-8drv: Product structure of SARS-CoV-2 Mpro C145A mutant in complex with... -

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基本情報

登録情報
データベース: PDB / ID: 8drv
タイトルProduct structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp8-nsp9 (C8) cut site sequence
要素Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) 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) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / 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) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / 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 / double membrane vesicle viral factory outer membrane / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase 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 / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase 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 / regulation of autophagy / host cell perinuclear region of cytoplasm / 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 / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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 / 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. / : / : / Coronavirus replicase NSP7
類似検索 - ドメイン・相同性
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: 2.4 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

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) cut site
B: Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) cut site
C: Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) cut site
D: Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)135,4455
ポリマ－135,2064
非ポリマー2381
水4,450247
1
A: Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) cut site
C: Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) cut site


分子量 (理論値)分子数
合計 (水以外)67,6032
ポリマ－67,6032
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-13 kcal/mol
Surface area26030 Å2
手法PISA
2
B: Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) cut site
D: Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,8413
ポリマ－67,6032
非ポリマー2381
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-11 kcal/mol
Surface area25860 Å2
手法PISA
単位格子
Length a, b, c (Å)85.788, 117.202, 121.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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要素

#1: タンパク質
Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) 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 / nsp8


分子量: 33801.570 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: rep, 1a-1b / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: 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: 1 / 由来タイプ: 合成 / 式: C10H22O6 / コメント: 沈殿剤*YM
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 247 / 由来タイプ: 天然 / 式: H2O
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: 2.27 Å3/Da / 溶媒含有率: 45.87 %
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 Tris pH 8.5, 20% PEG 3350

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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: 1.033 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年4月10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: 2.2→60.69 Å / Num. obs: 62720 / % possible obs: 99.9 % / 冗長度: 12.5 % / Biso Wilson estimate: 46.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.181 / Net I/σ(I): 9.9
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
2.2-2.2611.32.8525155545460.384199.6
9.84-49.5511.40.04791758060.99938.199.3

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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
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 7JOY

7joy


解像度: 2.4→60.69 Å / SU ML: 0.32 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 25.28 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2398 2441 5.04 %
Rwork0.1776 46032 -
obs0.1808 48473 99.84 %
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 max: 140.24 Å2 / Biso mean: 53.7053 Å2 / Biso min: 26.75 Å2
精密化ステップサイクル: final / 解像度: 2.4→60.69 Å
タンパク質核酸リガンド溶媒全体
原子数9376 0 10 247 9633
Biso mean--55.52 48.31 -
残基数----1217
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.450.32121410.281726682809100
2.45-2.50.38951160.259427022818100
2.5-2.560.29181530.235226722825100
2.56-2.620.30021270.230926682795100
2.62-2.70.31251330.22927082841100
2.7-2.770.31331250.226526962821100
2.77-2.860.31091330.244726982831100
2.86-2.970.30791420.251726962838100
2.97-3.090.33891270.225326892816100
3.09-3.230.29081560.2122656281299
3.23-3.40.26161420.19862675281799
3.4-3.610.22931360.186527152851100
3.61-3.890.25651830.169326782861100
3.89-4.280.2231500.140627362886100
4.28-4.90.17521550.125827402895100
4.9-6.170.18571690.144227582927100
6.17-60.690.17661530.13382877303099
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)
12.7862.9014-0.42744.7859-0.6972.59340.1411-0.2468-0.0803-0.1479-0.18-0.09020.14550.03530.04650.26890.0477-0.01420.31820.01830.227-2.41429.11516.1989
29.4116-0.65165.29264.8631-2.10617.2489-0.0610.24510.49220.1616-0.4785-0.6073-0.20370.30230.57680.35540.00030.03970.33650.10090.354412.254641.701416.7608
32.2351.8076-0.08716.0326-0.75122.06040.0896-0.10420.1679-0.1081-0.05780.2043-0.1451-0.2362-0.04550.21180.06130.02620.2906-0.02160.2495-3.852334.409518.6781
41.27641.2122-1.27534.9428-0.56994.5076-0.02530.1605-0.15720.087-0.1562-0.13920.06110.01510.20290.2056-0.008-0.01550.34210.04020.2911-1.316421.368722.691
54.052-0.38253.07934.349-1.153.2454-0.1468-0.2926-0.12590.2021-0.0824-0.43240.10520.24460.23150.2403-0.00020.02530.29460.08950.24412.680726.962625.2905
62.18911.6148-0.62731.2632-0.38720.13170.4122-0.6778-0.76670.7482-0.7899-0.8136-0.36760.48880.41310.44-0.1519-0.15130.60140.22660.531410.675724.446931.7152
72.76550.82080.83666.53722.06044.0268-0.10080.0656-0.14580.10550.61840.60240.9439-0.3505-0.55840.5403-0.1218-0.06690.43590.14190.4436-8.99220.838338.5151
84.53081.5985-3.0147.8828-0.8954.64040.0725-1.1319-0.22250.9598-0.3022-0.1319-0.68941.02280.31270.4943-0.0959-0.07250.60860.12140.38981.31578.815946.6759
99.4136-0.3675-0.45994.4255-0.81985.93390.2527-0.5236-0.34940.38770.37820.51310.0296-1.301-0.55370.35390.02430.08470.59230.19230.4118-9.6174.743843.0222
105.08131.8578-3.25310.9195-0.76493.5372-0.10630.77130.4842-0.03480.22330.1230.221-0.0674-0.13960.4589-0.0163-0.07360.45330.09580.3692-10.16824.784331.379
111.7803-2.94521.61667.0699-1.94812.5026-0.12030.07190.15350.4162-0.0378-0.154-0.2729-0.01370.15250.27170.02870.02420.30960.02630.245540.73572.098342.714
125.328-0.3648-1.14125.444-0.87299.13760.12380.00980.0696-0.0959-0.1649-0.22480.31550.56490.02110.32080.0617-0.03820.29930.05050.385650.5198-10.62344.226
134.58140.5158-2.73936.1947-4.29156.1909-0.09790.3759-0.339-0.29750.48870.74470.2112-1.2582-0.36390.26320.0552-0.05030.40790.02280.358633.2874-1.939537.4671
141.935-0.97920.9195.0889-0.94266.1762-0.0798-0.06580.1320.1746-0.03350.0464-0.0954-0.25020.11710.29360.0428-0.0290.33790.02110.330241.23548.305836.129
153.1688-0.25050.51233.7462-1.53014.35460.2340.1469-0.0487-0.3394-0.4102-0.35340.01940.53960.15450.31350.09830.01160.40330.09260.315747.99892.718229.5676
164.4578-0.6308-2.0742.92942.03982.6678-0.1060.07980.3249-0.46680.06680.1697-0.9006-0.02720.03860.4860.0511-0.02320.31920.05170.342230.987525.497115.6806
172.5697-2.0752-1.86625.96521.77514.05540.11410.316-0.3906-0.5239-0.25640.22750.03610.13020.12150.40840.0417-0.03680.38370.05680.393333.616218.141810.9678
185.2539-1.51640.91161.38270.75352.9763-0.2019-0.529-0.39450.19270.36490.2578-0.18920.2768-0.18830.4616-0.0176-0.01570.34480.03490.41231.557523.432823.5164
196.65570.83082.46711.82790.25072.2475-0.0521-0.15740.0057-0.10090.03760.029-0.0488-0.26560.00560.32980.0276-0.01090.278-0.00690.2164-18.858212.29178.0298
205.8417-0.27781.13532.1457-0.44071.99340.0389-0.2653-0.2635-0.22960.04090.31590.2934-0.3407-0.08130.3881-0.017-0.02970.33040.00720.1967-26.62167.79191.8118
213.2782-0.48050.58592.95461.11541.83350.0995-0.1934-0.38010.1781-0.02940.13080.2646-0.096-0.07180.39330.02110.00260.30870.04110.334-13.83652.538310.5028
221.2769-0.6901-0.23280.99691.45772.7214-0.2571-0.34960.13140.5520.7204-0.88950.45440.7823-0.36220.52930.2363-0.07320.5943-0.12540.825215.20720.235115.3791
235.4151-1.542-1.07184.85192.7785.06590.0158-0.32130.11730.22480.1319-0.47960.57250.6632-0.14390.42660.1420.04950.45830.06190.499810.1914-2.244912.8497
245.9071-2.7772-2.86481.8490.87122.121-0.034-0.32740.11660.26740.16520.0482-0.1565-0.1045-0.110.47080.0628-0.03310.5289-0.01060.414924.058220.140248.3634
253.20040.57780.54318.8298-2.68522.65830.2111-0.46950.5077-0.19890.13860.6128-0.5137-0.6536-0.39690.63250.220.03350.79140.07450.73158.035930.23250.5084
264.6854-2.208-2.28027.4591-0.51942.0725-0.3907-0.6951-0.25550.65420.32830.3843-0.1923-0.06120.06080.51290.1235-0.00680.66360.00840.268116.907919.708457.5989
274.60852.0046-0.5663.7520.56131.7973-0.0041-0.08020.4191-0.00640.02080.0382-0.36860.171-0.02630.58650.0836-0.06830.4605-0.00730.467229.561929.302845.0926
283.6948-0.67921.44248.96232.17823.33060.212-0.3936-0.05270.2432-0.0782-0.7532-0.15980.0374-0.11880.4976-0.16-0.07780.60960.04680.536754.993934.952239.1137
297.87351.29310.0888.250.88438.32840.25420.32760.0669-0.82060.16680.2791-0.30640.591-0.38970.4816-0.0388-0.05410.3889-0.03890.41752.572729.792635.3561
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 120 )A71 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 155 )A121 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 180 )A156 - 180
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 200 )A181 - 200
7X-RAY DIFFRACTION7chain 'A' and (resid 201 through 226 )A201 - 226
8X-RAY DIFFRACTION8chain 'A' and (resid 227 through 243 )A227 - 243
9X-RAY DIFFRACTION9chain 'A' and (resid 244 through 274 )A244 - 274
10X-RAY DIFFRACTION10chain 'A' and (resid 275 through 306 )A275 - 306
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 43 )B1 - 43
12X-RAY DIFFRACTION12chain 'B' and (resid 44 through 91 )B44 - 91
13X-RAY DIFFRACTION13chain 'B' and (resid 92 through 110 )B92 - 110
14X-RAY DIFFRACTION14chain 'B' and (resid 111 through 155 )B111 - 155
15X-RAY DIFFRACTION15chain 'B' and (resid 156 through 200 )B156 - 200
16X-RAY DIFFRACTION16chain 'B' and (resid 201 through 226 )B201 - 226
17X-RAY DIFFRACTION17chain 'B' and (resid 227 through 274 )B227 - 274
18X-RAY DIFFRACTION18chain 'B' and (resid 275 through 306 )B275 - 306
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 43 )C1 - 43
20X-RAY DIFFRACTION20chain 'C' and (resid 44 through 110 )C44 - 110
21X-RAY DIFFRACTION21chain 'C' and (resid 111 through 200 )C111 - 200
22X-RAY DIFFRACTION22chain 'C' and (resid 201 through 226 )C201 - 226
23X-RAY DIFFRACTION23chain 'C' and (resid 227 through 302 )C227 - 302
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 43 )D1 - 43
25X-RAY DIFFRACTION25chain 'D' and (resid 44 through 70 )D44 - 70
26X-RAY DIFFRACTION26chain 'D' and (resid 71 through 100 )D71 - 100
27X-RAY DIFFRACTION27chain 'D' and (resid 101 through 200 )D101 - 200
28X-RAY DIFFRACTION28chain 'D' and (resid 201 through 257 )D201 - 257
29X-RAY DIFFRACTION29chain 'D' and (resid 258 through 302 )D258 - 302

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る