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- PDB-8ds1: Structure of SARS-CoV-2 Mpro in complex with nsp12-nsp13 (C12) cu... -

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基本情報

登録情報
データベース: PDB / ID: 8ds1
タイトルStructure of SARS-CoV-2 Mpro in complex with nsp12-nsp13 (C12) cut site sequence
要素3C-like proteinase nsp5
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 / 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; - / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / 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; - / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / 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 / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / mRNA (guanine-N7)-methyltransferase / omega peptidase activity / methyltransferase cap1 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / 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 / host cell perinuclear region of cytoplasm / single-stranded RNA binding / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / lipid binding / DNA-templated transcription / 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
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 Nonstructural protein 13, 1B domain ...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 Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus Nsp12 Interface domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) 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 / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / 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 / 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 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / Coronavirus 3Ecto domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / : / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus replicase NSP7 / Peptidase family C16 domain profile.
類似検索 - ドメイン・相同性
DI(HYDROXYETHYL)ETHER / 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: 2.19 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28日Provider: repository / タイプ: Initial release
改定 1.12022年10月12日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22023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

ダウンロードとリンク

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集合体

登録構造単位
A: 3C-like proteinase nsp5
B: 3C-like proteinase nsp5
C: 3C-like proteinase nsp5
D: 3C-like proteinase nsp5
E: 3C-like proteinase nsp5
F: 3C-like proteinase nsp5
G: 3C-like proteinase nsp5
H: 3C-like proteinase nsp5
I: 3C-like proteinase nsp5
J: 3C-like proteinase nsp5
K: 3C-like proteinase nsp5
L: 3C-like proteinase nsp5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)407,23722
ポリマ－406,59212
非ポリマー64610
水5,152286
1
A: 3C-like proteinase nsp5
B: 3C-like proteinase nsp5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,8944
ポリマ－67,7652
非ポリマー1292
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-21 kcal/mol
Surface area25100 Å2
手法PISA
2
C: 3C-like proteinase nsp5
D: 3C-like proteinase nsp5


分子量 (理論値)分子数
合計 (水以外)67,7652
ポリマ－67,7652
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-10 kcal/mol
Surface area26020 Å2
手法PISA
3
E: 3C-like proteinase nsp5
F: 3C-like proteinase nsp5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,8944
ポリマ－67,7652
非ポリマー1292
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-22 kcal/mol
Surface area25040 Å2
手法PISA
4
G: 3C-like proteinase nsp5
H: 3C-like proteinase nsp5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,8944
ポリマ－67,7652
非ポリマー1292
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-22 kcal/mol
Surface area24970 Å2
手法PISA
5
I: 3C-like proteinase nsp5
J: 3C-like proteinase nsp5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,8713
ポリマ－67,7652
非ポリマー1061
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-9 kcal/mol
Surface area26160 Å2
手法PISA
6
K: 3C-like proteinase nsp5
L: 3C-like proteinase nsp5
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,9175
ポリマ－67,7652
非ポリマー1523
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-36 kcal/mol
Surface area25110 Å2
手法PISA
単位格子
Length a, b, c (Å)67.001, 105.783, 276.341
Angle α, β, γ (deg.)90.000, 90.930, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
3C-like proteinase nsp5 / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


分子量: 33882.660 Da / 分子数: 12 / 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-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 5 / 由来タイプ: 合成 / 式: Na
#3: 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: 5 / 由来タイプ: 合成 / 式: C4H10O3
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 286 / 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: 2.41 Å3/Da / 溶媒含有率: 48.92 %
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: 0.15M DL-Malic acid (pH 7.0), 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: CLSI / ビームライン: 08B1-1 / 波長: 1.18 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2021年9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: 1.18 Å / 相対比: 1
反射解像度: 2.19→48.52 Å / Num. obs: 150463 / % possible obs: 99.8 % / 冗長度: 6.8 % / Biso Wilson estimate: 38.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.134 / Net I/σ(I): 10.9
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
2.4-2.446.92.1095019773270.469199.7
13.15-48.5260.02557769560.99941.297.8

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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
精密化構造決定の手法: 分子置換
開始モデル: 7JOY

7joy


解像度: 2.19→48.52 Å / SU ML: 0.29 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 32.45 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2484 6702 5.04 %
Rwork0.1979 126356 -
obs0.2005 133058 67.31 %
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: 202.24 Å2 / Biso mean: 53.8466 Å2 / Biso min: 11.94 Å2
精密化ステップサイクル: final / 解像度: 2.19→48.52 Å
タンパク質核酸リガンド溶媒全体
原子数27932 0 40 286 28258
Biso mean--54.33 37.97 -
残基数----3636
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.220.3839160.3094584747
2.22-2.240.3592190.2935926119
2.24-2.270.3273330.276180784013
2.27-2.30.3779460.28821212125819
2.3-2.330.361840.29821473155724
2.33-2.360.35591060.29351866197230
2.36-2.40.29391260.30542218234436
2.4-2.430.33081100.30342353246338
2.43-2.470.36771310.30082708283943
2.47-2.510.32741570.31232869302646
2.51-2.550.32352050.31463159336451
2.55-2.60.38292000.2913459365956
2.6-2.650.35581850.28913778396360
2.65-2.70.34641780.2834096427465
2.7-2.760.33142200.27124325454570
2.76-2.830.32992820.28244744502676
2.83-2.90.31873160.27415208552484
2.9-2.970.32053130.26525718603192
2.98-3.060.28453300.26056164649498
3.06-3.160.32253270.258762156542100
3.16-3.270.2853000.231762636563100
3.27-3.410.2733340.206462476581100
3.41-3.560.26093240.197162876611100
3.56-3.750.24663430.180362566599100
3.75-3.980.2333260.16662626588100
3.98-4.290.19813570.145362626619100
4.29-4.720.1933300.136863066636100
4.72-5.40.18713260.143263036629100
5.4-6.810.22383210.178463536674100
6.81-48.520.17583570.15246395675299
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)
11.3572-0.69751.40341.70290.28643.7165-0.2813-0.34790.41910.5221-0.0523-0.2361-0.25750.01310.28530.3692-0.0528-0.06120.3799-0.09510.283520.966667.9295168.1974
20.9488-0.08320.10280.01740.09830.9762-0.5003-0.77960.53360.57570.2358-0.0209-0.5095-0.54080.21240.59380.0984-0.00240.6557-0.2070.298114.181167.4671174.8917
31.6516-0.5678-0.42742.91460.29683.80150.0191-0.15780.18270.3261-0.0487-0.0520.12830.02940.02560.2232-0.02630.00110.2588-0.04360.192621.067260.4754157.0635
43.6364-1.15081.96633.2360.26443.17690.18030.1804-0.0999-0.3515-0.17560.12520.15570.24360.00410.24510.0555-0.03490.2328-0.00740.177616.549448.7788134.7123
50.9234-0.71631.11.3535-0.51391.43780.0004-0.26620.23430.1005-0.10370.3103-0.1125-0.46020.09380.20880.03780.09820.4553-0.11920.336-3.378572.687146.9437
63.3144-1.36510.77432.5041-1.45424.0803-0.21020.09450.1329-0.2766-0.05090.39440.5479-0.5210.24040.3148-0.0214-0.0560.8228-0.06590.5981-19.883472.2674136.7197
72.6424-1.2263-0.32811.74360.22271.72570.0127-0.16020.52840.0909-0.01390.1789-0.1505-0.26-0.01490.16010.0390.01350.4161-0.1120.3931-1.759675.8202143.0229
83.63361.88610.92751.3496-0.06952.4303-0.19230.0291-0.4797-0.1138-0.02-0.3847-0.26430.46260.1460.2222-0.03120.04630.34750.03310.478922.523678.4249132.0531
92.3969-1.9612-0.76815.06712.14214.0255-0.2666-0.0061-0.59680.41170.16870.59940.6062-0.06130.06210.34350.05940.06240.34330.03550.26057.828736.7032104.8773
101.56921.6130.76112.55451.6071.1214-0.4117-0.3877-0.15210.2109-0.2051.41940.316-0.35670.50040.57210.02250.27160.6901-0.01071.1972-16.406152.9034119.6721
111.6773-0.14720.10251.31480.01671.26-0.2504-0.05550.12360.02810.1373-0.0598-0.9079-0.05940.07410.82860.031-0.15690.4160.02430.215411.784266.162104.1162
122.5771-0.86181.13332.9591-2.62282.3824-0.0082-0.23270.6101-0.27280.05220.4757-1.0322-0.36450.06821.68590.0276-0.59340.5251-0.05951.027813.249286.7545108.7643
131.4710.2686-0.07431.16760.0261.1907-0.2190.15330.25020.14720.1826-0.0134-0.62990.1569-0.0130.8895-0.0853-0.10660.47710.1030.434217.927770.814100.6375
142.9710.6580.86621.4558-1.25172.1489-0.3179-0.04940.5009-0.1605-0.14760.0763-0.7539-0.2860.36940.82760.1697-0.16850.40640.01380.35243.317863.8501101.8945
152.9618-0.10970.55512.93990.30321.1443-0.654-0.04050.4196-0.16260.17390.7449-0.8422-0.40560.43540.83150.2213-0.21080.58940.04240.5364-5.79766.046594.9195
161.38041.11070.38950.89990.39091.0408-0.25410.61790.27220.43320.57811.5485-0.8124-0.1083-0.17660.99490.3235-0.31890.88630.24131.2374-19.568765.714884.7551
172.1274-2.04540.65821.9908-0.54930.4832-0.33740.687-0.0726-0.67420.13981.7629-0.4151-0.36710.10860.77610.1629-0.39511.0273-0.12031.1079-15.174254.999281.6648
181.6645-0.4193-0.10773.96140.69272.5705-0.1727-0.0780.12970.82920.25680.65040.0044-0.2972-0.06370.49480.1583-0.01430.58630.02890.6868-9.673650.518490.7137
191.47740.5194-0.37682.4585-0.96842.1382-0.245-0.02480.0793-0.39720.14920.53060.2346-0.3240.09070.2256-0.0635-0.09430.40070.02820.31810.014132.137261.3631
201.42151.5521-1.71611.6986-1.7034.4481-0.0279-0.01260.76150.00180.080.8669-0.4634-0.63840.11290.2719-0.0772-0.02821.02440.10750.7096-16.867533.293971.0817
211.8520.50810.26170.8604-0.062.19060.01110.6255-0.2283-0.31860.2690.59650.2799-0.2724-0.18630.4805-0.3503-0.16010.64750.05860.5994-9.672526.491558.1996
222.74461.6080.63252.507-0.4274.5123-0.0347-0.0776-0.3196-0.34980.27490.21860.0762-0.0753-0.19740.1846-0.0364-0.03170.32070.01660.29847.34730.662166.8577
234.3052-0.54250.57820.9471-0.89281.4428-0.2027-0.6911-0.02120.00730.20660.08650.0964-0.18240.00210.1587-0.01950.01470.2857-0.02750.26958.660429.884875.0642
242.0839-1.31010.14981.28860.12192.8992-0.1958-0.4999-0.13280.1169-0.0249-0.17620.41850.80420.22270.2690.07010.03410.6110.09980.406331.074424.121578.7791
253.7611-0.9221-0.12.3349-1.48434.4999-0.18810.67080.63210.1274-0.0228-0.2178-0.24320.59920.18950.2404-0.0073-0.05230.35230.07330.437729.535531.184474.0054
262.3740.8237-0.17312.8083-0.39161.8408-0.07680.23080.0452-0.4724-0.19150.04021.00390.09110.21090.45320.1147-0.02440.26310.01830.191519.039237.336745.8078
271.48071.0985-1.05593.46650.62361.49850.11980.3356-0.6636-1.3647-0.3811-1.14410.73230.53290.02191.14530.2980.3380.71420.0870.676635.396538.224932.2189
281.71630.6272-0.39211.9208-0.43253.7952-0.0082-0.1432-0.0421-0.406-0.1734-0.01810.33760.03070.13030.3620.1016-0.01330.20290.05310.167920.854541.485746.5898
291.20780.09210.82352.30491.72612.44660.0703-0.1690.2070.4472-0.17470.06550.13850.3520.13530.4606-0.09530.03740.26390.06240.304325.411355.868368.0036
302.89770.9814-0.64383.46530.67681.90960.0585-0.11780.10520.8454-0.20930.16810.28320.03920.10730.6082-0.08190.0120.2304-0.00430.34319.730858.708274.0201
313.1840.1395-0.12894.06950.08773.472-0.10250.856-0.52450.7332-0.03730.89590.1663-0.40170.08260.5687-0.04930.13630.5127-0.06240.518214.583550.051167.0707
321.0807-0.25930.15871.6984-0.1612.38880.0604-0.0757-0.03340.3198-0.0724-0.0398-0.17750.25670.00050.26730.0233-0.02730.1959-0.00430.180217.656264.795825.0494
332.6186-0.9288-0.65181.95950.73711.75-0.119-0.89280.34070.790.2395-0.76220.20330.7175-0.08530.82540.0458-0.26370.6759-0.09020.541431.974165.41738.3703
341.1674-0.6455-0.21671.79450.17772.7769-0.1601-0.0650.04060.25340.093-0.08170.10790.22720.06470.2160.0267-0.04310.12420.04580.157620.150360.162823.9594
350.73530.0047-0.33391.28941.00682.4302-0.0180.03010.035-0.0170.0806-0.130.01240.373-0.02830.13410.0166-0.02870.1280.05370.195224.944448.16721.7051
363.101-1.2361.66672.25290.36452.3790.02560.35690.1677-0.16780.03120.15710.04610.303-0.03560.14960.0005-0.00910.09060.00170.215419.499445.7272-4.3323
374.33981.91710.53153.8677-0.43343.66650.1172-0.56030.72520.3109-0.25960.353-0.3364-0.3592-0.0810.2949-0.0341-0.03810.204-0.0030.334313.919553.27243.4793
381.1221-0.76190.69761.3011-0.78781.8986-0.05450.0156-0.23950.1588-0.0220.10410.0332-0.21080.07460.1135-0.03520.03070.20750.0210.2031-0.848170.49569.9389
393.0384-1.6910.49941.8192-2.09183.80270.06710.165-0.6491-0.2524-0.00760.44520.5561-0.6749-0.02250.15460.00970.00450.5102-0.0970.4744-17.575970.5274-0.1685
402.6912-0.4847-0.43881.1728-0.08152.3232-0.12750.0075-0.03370.09670.01070.07240.0381-0.22210.11790.1169-0.0014-0.01560.111-0.00670.22510.961873.71273.4534
414.88041.40590.41132.12330.29261.9088-0.04560.3611-0.6603-0.1407-0.0082-0.0915-0.08060.26120.0296-0.1448-0.2454-0.03840.17640.11580.452429.504477.1123-3.9575
421.5697-0.21650.21351.3201-0.00052.1388-0.06520.15880.00390.07920.0302-0.13940.19970.39420.05710.2448-0.01660.05130.24790.01940.17712.113940.9117-35.1099
432.99760.0012-0.20642.42950.83831.8941-0.18090.4562-0.4927-0.34750.149-0.19560.58860.23160.01440.52430.10590.07230.3838-0.03590.358317.778626.3097-38.5561
443.37880.2029-0.1241.57520.08421.9537-0.15850.095-0.1738-0.04120.02630.1290.3156-0.00360.11070.3059-0.04220.04280.1985-0.01010.1714.220338.3573-30.8425
452.0391-0.5151-0.61941.52260.54092.05310.2256-0.83360.21040.5123-0.43081.30160.1844-0.45610.10990.4472-0.17470.26520.6289-0.20670.7878-17.465549.2913-15.1924
460.28840.0757-0.70332.90470.84232.0837-0.20310.2352-0.1148-0.5438-0.05310.4959-0.33860.10830.21130.25950.0176-0.06210.3015-0.09020.36-10.273355.2139-21.6305
471.4649-0.40720.35741.4102-0.89482.0669-0.12730.07050.2151-0.1158-0.0184-0.1139-0.54860.28670.12140.3268-0.1316-0.07430.3578-0.00010.125111.214865.7485-32.9941
481.8937-0.28670.62582.1893-0.17571.0923-0.4307-0.11790.52520.21460.1613-0.271-0.63260.19180.2530.6907-0.1972-0.14880.35480.03730.497316.99178.0354-30.6623
493.1453-0.02750.70543.2036-0.40852.2163-0.22960.18990.2469-0.01580.01060.2497-0.5870.05650.18520.3952-0.0306-0.07070.2066-0.01840.20551.048268.0687-36.5297
503.022-1.229-0.87710.51130.43350.7244-0.47780.6166-0.8334-0.20320.01631.65420.6356-0.5779-0.0240.59-0.1789-0.04340.5533-0.21210.8918-17.175349.6425-49.3124
511.082-1.13290.00883.28981.82631.6057-0.37371.086-0.3815-0.9139-0.40552.1095-0.6105-0.65680.52390.64440.0118-0.29570.675-0.18230.9448-18.373757.9392-52.4242
521.04780.59741.79785.10831.89353.235-0.3011-0.06480.20670.81060.28130.47350.4999-0.0986-0.04510.4208-0.0180.06010.35860.03370.3199-9.834449.326-45.7895
534.96341.6624-1.28241.8338-0.18211.5107-0.20070.1781-0.0384-0.1042-0.09770.2840.0414-0.39370.23670.2902-0.0137-0.02670.3442-0.10010.2647-6.77534.9257-73.5702
542.52290.50910.28871.06310.07862.2549-0.24830.2131-0.1932-0.1111-0.05290.12950.1125-0.28240.26630.2445-0.08920.06670.2262-0.10060.25261.907231.691-71.3151
554.9253-1.1264-0.7022.98720.75242.3990.0111-0.30110.13820.23830.0177-0.0004-0.03090.2666-0.03730.20720.03530.07610.26040.03590.295830.360727.7123-64.1467
561.49590.706-0.43192.17460.20334.0608-0.16990.2006-0.097-0.49020.1106-0.19080.41120.0830.02210.3509-0.03110.05510.2628-0.03020.137123.614644.6425-91.5675
573.67921.4632-0.09694.45720.83522.72240.069-0.35010.28620.6013-0.44050.53920.1241-0.34710.32740.437-0.08590.05960.3649-0.09820.319719.914158.6987-63.428
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 70 )A1 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 99 )A71 - 99
3X-RAY DIFFRACTION3chain 'A' and (resid 100 through 200 )A100 - 200
4X-RAY DIFFRACTION4chain 'A' and (resid 201 through 302 )A201 - 302
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 43 )B1 - 43
6X-RAY DIFFRACTION6chain 'B' and (resid 44 through 70 )B44 - 70
7X-RAY DIFFRACTION7chain 'B' and (resid 71 through 180 )B71 - 180
8X-RAY DIFFRACTION8chain 'B' and (resid 181 through 302 )B181 - 302
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 200 )C1 - 200
10X-RAY DIFFRACTION10chain 'C' and (resid 201 through 306 )C201 - 306
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 43 )D1 - 43
12X-RAY DIFFRACTION12chain 'D' and (resid 44 through 66 )D44 - 66
13X-RAY DIFFRACTION13chain 'D' and (resid 67 through 110 )D67 - 110
14X-RAY DIFFRACTION14chain 'D' and (resid 111 through 155 )D111 - 155
15X-RAY DIFFRACTION15chain 'D' and (resid 156 through 226 )D156 - 226
16X-RAY DIFFRACTION16chain 'D' and (resid 227 through 243 )D227 - 243
17X-RAY DIFFRACTION17chain 'D' and (resid 244 through 273 )D244 - 273
18X-RAY DIFFRACTION18chain 'D' and (resid 274 through 306 )D274 - 306
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 43 )E1 - 43
20X-RAY DIFFRACTION20chain 'E' and (resid 44 through 70 )E44 - 70
21X-RAY DIFFRACTION21chain 'E' and (resid 71 through 100 )E71 - 100
22X-RAY DIFFRACTION22chain 'E' and (resid 101 through 155 )E101 - 155
23X-RAY DIFFRACTION23chain 'E' and (resid 156 through 213 )E156 - 213
24X-RAY DIFFRACTION24chain 'E' and (resid 214 through 260 )E214 - 260
25X-RAY DIFFRACTION25chain 'E' and (resid 261 through 302 )E261 - 302
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 43 )F1 - 43
27X-RAY DIFFRACTION27chain 'F' and (resid 44 through 66 )F44 - 66
28X-RAY DIFFRACTION28chain 'F' and (resid 67 through 180 )F67 - 180
29X-RAY DIFFRACTION29chain 'F' and (resid 181 through 237 )F181 - 237
30X-RAY DIFFRACTION30chain 'F' and (resid 238 through 284 )F238 - 284
31X-RAY DIFFRACTION31chain 'F' and (resid 285 through 302 )F285 - 302
32X-RAY DIFFRACTION32chain 'G' and (resid 1 through 42 )G1 - 42
33X-RAY DIFFRACTION33chain 'G' and (resid 43 through 70 )G43 - 70
34X-RAY DIFFRACTION34chain 'G' and (resid 71 through 180 )G71 - 180
35X-RAY DIFFRACTION35chain 'G' and (resid 181 through 237 )G181 - 237
36X-RAY DIFFRACTION36chain 'G' and (resid 238 through 284 )G238 - 284
37X-RAY DIFFRACTION37chain 'G' and (resid 285 through 302 )G285 - 302
38X-RAY DIFFRACTION38chain 'H' and (resid 1 through 43 )H1 - 43
39X-RAY DIFFRACTION39chain 'H' and (resid 44 through 70 )H44 - 70
40X-RAY DIFFRACTION40chain 'H' and (resid 71 through 200 )H71 - 200
41X-RAY DIFFRACTION41chain 'H' and (resid 201 through 302 )H201 - 302
42X-RAY DIFFRACTION42chain 'I' and (resid 1 through 43 )I1 - 43
43X-RAY DIFFRACTION43chain 'I' and (resid 44 through 91 )I44 - 91
44X-RAY DIFFRACTION44chain 'I' and (resid 92 through 200 )I92 - 200
45X-RAY DIFFRACTION45chain 'I' and (resid 201 through 274 )I201 - 274
46X-RAY DIFFRACTION46chain 'I' and (resid 275 through 306 )I275 - 306
47X-RAY DIFFRACTION47chain 'J' and (resid 1 through 43 )J1 - 43
48X-RAY DIFFRACTION48chain 'J' and (resid 44 through 100 )J44 - 100
49X-RAY DIFFRACTION49chain 'J' and (resid 101 through 200 )J101 - 200
50X-RAY DIFFRACTION50chain 'J' and (resid 201 through 226 )J201 - 226
51X-RAY DIFFRACTION51chain 'J' and (resid 227 through 274 )J227 - 274
52X-RAY DIFFRACTION52chain 'J' and (resid 275 through 306 )J275 - 306
53X-RAY DIFFRACTION53chain 'K' and (resid 1 through 70 )K1 - 70
54X-RAY DIFFRACTION54chain 'K' and (resid 71 through 200 )K71 - 200
55X-RAY DIFFRACTION55chain 'K' and (resid 201 through 302 )K201 - 302
56X-RAY DIFFRACTION56chain 'L' and (resid 1 through 213 )L1 - 213
57X-RAY DIFFRACTION57chain 'L' and (resid 214 through 302 )L214 - 302

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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://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