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基本情報

登録情報
データベース: PDB / ID: 8dry
タイトルProduct structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp12-nsp13 (C12) cut site sequence
要素Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) 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 / 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 / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / 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 / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / 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 / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Lipocalin signature. / (+) 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 Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus 3Ecto domain profile. / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus
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: 2.49 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 nsp12-nsp13 (C12) cut site
B: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
C: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
D: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
E: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
F: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
G: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
H: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
I: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
J: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
K: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
L: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)406,41914
ポリマ－406,20712
非ポリマー2122
水2,864159
1
A: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
B: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,8073
ポリマ－67,7012
非ポリマー1061
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-9 kcal/mol
Surface area25490 Å2
手法PISA
2
C: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
D: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site


分子量 (理論値)分子数
合計 (水以外)67,7012
ポリマ－67,7012
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-12 kcal/mol
Surface area26340 Å2
手法PISA
3
E: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
F: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)67,8073
ポリマ－67,7012
非ポリマー1061
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-12 kcal/mol
Surface area25740 Å2
手法PISA
4
G: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
H: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site


分子量 (理論値)分子数
合計 (水以外)67,7012
ポリマ－67,7012
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-12 kcal/mol
Surface area25470 Å2
手法PISA
5
I: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
J: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site


分子量 (理論値)分子数
合計 (水以外)67,7012
ポリマ－67,7012
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-13 kcal/mol
Surface area26820 Å2
手法PISA
6
K: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
L: Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site


分子量 (理論値)分子数
合計 (水以外)67,7012
ポリマ－67,7012
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-12 kcal/mol
Surface area25230 Å2
手法PISA
単位格子
Length a, b, c (Å)67.329, 107.923, 277.248
Angle α, β, γ (deg.)90.000, 90.730, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) 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 / Pol / RdRp / Non-structural protein 12 / nsp12


分子量: 33850.594 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, RNA-directed RNA polymerase
#2: 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: 2 / 由来タイプ: 合成 / 式: C4H10O3
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 159 / 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: 2.48 Å3/Da / 溶媒含有率: 50.39 %
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: 0.9M CHES (pH 9.5), 20% PEG 8K

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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7月28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: 2.49→65.23 Å / Num. obs: 100601 / % possible obs: 72.6 % / 冗長度: 7 % / CC1/2: 0.997 / Net I/σ(I): 9.1
反射 シェル解像度: 2.49→2.58 Å / 冗長度: 7.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5918 / CC1/2: 0.628 / % possible all: 62

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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
PDB_EXTRACT3.27データ抽出
Aimlessデータスケーリング
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: 2.49→65.23 Å / SU ML: 0.34 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 33.87 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2641 2006 1.99 %
Rwork0.1942 98559 -
obs0.1956 100565 72.55 %
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: 184.59 Å2 / Biso mean: 59.4288 Å2 / Biso min: 15.31 Å2
精密化ステップサイクル: final / 解像度: 2.49→65.23 Å
タンパク質核酸リガンド溶媒全体
原子数28114 0 14 159 28287
Biso mean--50.81 43.66 -
残基数----3644
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 (%)
2.49-2.550.568460.31362672733
2.55-2.620.387180.34211040105811
2.62-2.70.2934530.33972472252525
2.7-2.790.3393800.31424022410242
2.79-2.890.3791270.30286027615463
2.89-30.35641610.27747775793681
3-3.140.35221770.26498839901691
3.14-3.310.33661940.26189588978299
3.31-3.510.30062000.235497209920100
3.51-3.780.30231980.195696659863100
3.78-4.160.24621990.165897509949100
4.16-4.770.2141960.14297199915100
4.77-60.22811980.16597709968100
6-65.230.21511990.1611990510104100
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)
11.1207-0.7232-0.42022.26210.66283.1274-0.2492-0.39860.21570.7513-0.0612-0.4951-0.61960.46770.10960.5952-0.0559-0.15380.2984-0.02990.165121.49366.177170.793
22.4335-0.8488-0.71922.58460.42534.9093-0.1723-0.05610.02620.2185-0.0223-0.15850.08070.14250.17790.24030.0017-0.08580.15230.03120.124618.53560.615159.115
31.141-0.9965-0.60011.8981-0.05891.27240.1020.27410.0401-0.3317-0.1796-0.1340.04940.51930.03980.14580.0782-0.0760.21370.05490.274723.26949.328140.679
42.4529-1.11861.01394.2078-0.65343.1676-0.05620.09110.0004-0.3367-0.13030.0934-0.0004-0.1630.15090.18130.0779-0.09270.1736-0.02520.253216.49848.9136.449
51.1289-0.01090.22731.8915-0.63791.9588-0.2346-0.1784-0.16660.34030.11180.3985-0.2921-0.33130.08670.14070.04230.02740.3058-0.02550.2136-2.09771.946148.596
65.3894-0.2641-2.65082.7723-1.40835.0512-0.2411-0.0431-0.6919-0.2464-0.03950.170.3777-0.81770.24870.18480.1003-0.02680.4714-0.01410.6601-19.93572.75135.214
72.8254-0.3005-0.18121.6181-0.56832.4972-0.0979-0.103-0.01680.15640.10540.1977-0.263-0.25620.01070.12010.0293-0.00840.1556-0.01090.2194-1.1774.91142.275
81.27620.05071.14650.02330.11661.22820.221-0.1106-0.88580.2502-0.1965-0.77550.14470.59690.1239-0.2382-0.1185-0.33010.31360.14440.582932.04277.123135.973
93.55931.48160.26472.59210.12622.26990.0938-0.0031-0.21740.0056-0.2444-0.122-0.19160.16640.12340.1721-0.0953-0.11730.25270.05760.353426.58179.083134.094
102.85080.37050.12631.57870.68872.9746-0.08080.2108-0.11580.2192-0.1241-0.09370.25290.52810.2220.39240.0170.01320.23080.05840.155410.241.901103.482
115.65370.95880.0023.1866-0.09892.0082-0.1550.5347-1.2174-0.13390.09940.13721.00880.10820.03670.80050.10720.13440.5923-0.12530.561513.13623.58797.488
124.8153-0.216-0.12652.3597-0.15541.9301-0.0858-0.0726-0.32960.2296-0.05780.15050.43530.16720.1320.43930.05120.00340.19580.0110.18337.02739.699106.935
133.31531.3972-0.01081.7088-1.31241.5324-0.1891-0.12890.24860.4737-0.24211.430.3555-0.52240.24850.5225-0.22940.16560.4861-0.11890.7502-15.80543.96117.1
144.5820.9786-1.19430.79280.52631.3630.1831-1.1510.43450.5713-0.35761.12320.3913-0.1760.06960.5156-0.27140.21640.7363-0.15460.9099-17.86148.743124.592
150.203-0.0374-0.72080.80150.12652.5834-0.2856-0.0980.5432-0.44730.25260.78630.098-0.19420.06060.2667-0.0618-0.08290.4078-0.0390.7324-13.65355.137115.142
163.42750.44810.48942.97140.46761.9753-0.0788-0.08610.5236-0.1046-0.10430.1524-0.49970.05950.13060.4395-0.0717-0.09340.1978-0.0130.21835.80171.442104.335
172.8602-1.03760.00913.1681.78332.2184-0.26090.3706-0.8378-0.2113-0.27761.30780.0346-0.70750.46430.4616-0.0219-0.07530.4504-0.2230.861-18.14755.18888.447
185.05171.1677-1.0762.59690.03721.6869-0.21630.09790.2811-0.0848-0.02150.6161-0.0109-0.25110.18680.2175-0.0621-0.05080.2916-0.12290.394-8.55635.47764.962
192.59640.49820.91392.12570.13432.7781-0.13880.1571-0.2112-0.25910.08020.26050.1523-0.13070.04990.1721-0.06970.03380.1689-0.08080.28450.07732.39267.202
203.7554-1.4379-0.67783.84330.31532.9449-0.1177-0.05670.05850.07990.053-0.41820.15060.24990.05170.2570.09940.08790.2336-0.01190.394128.71728.5874.076
211.70630.0036-0.55631.811-0.13634.94290.0020.7028-0.1951-0.90460.009-0.40160.50250.446-0.02070.7754-0.06230.11930.6178-0.11580.37922.98241.03940.17
220.59510.38570.08622.61121.23325.1222-0.24870.3559-0.0606-0.56410.247-0.11480.14260.2076-0.04860.386-0.09140.02730.3403-0.04790.17521.46646.99447.587
232.34910.8623-1.3741.8154-0.88330.89310.1947-0.43530.36761.0101-0.31060.68960.23070.17040.12250.3971-0.13970.17890.2989-0.10650.349415.56558.39578.546
243.45070.3158-0.54753.80940.72262.62290.1795-0.17540.19280.4089-0.26250.25450.04880.00470.07850.2923-0.08190.02660.171-0.00320.175318.61259.7573.389
250.5751-0.5308-0.52561.7984-0.11320.7701-0.1745-0.4030.30870.3636-0.1844-0.0334-0.6558-0.84350.14160.58110.0388-0.07870.773-0.27360.370217.42569.02824.43
261.3496-1.5045-0.48113.54440.53814.4482-0.3108-0.38660.83940.683-0.0634-0.3821-0.6951-0.51380.30110.81110.061-0.14450.8272-0.21310.476824.25169.33937.298
271.2947-0.95170.05541.87450.12853.1331-0.06710.02270.0660.2945-0.23270.08610.1168-0.58340.29450.3446-0.1101-0.06330.5558-0.16940.347820.17562.33517.085
283.8126-0.41420.00116.08930.17598.27530.0305-0.7321-0.01850.1514-0.33650.2149-0.0586-0.71760.35620.43810.0155-0.09810.6038-0.21080.29717.76766.0719.449
292.0706-0.25641.97452.41891.89125.80130.23310.0415-0.13450.1915-0.0718-0.10630.29020.3195-0.16030.3057-0.0162-0.0860.5186-0.08890.313726.09858.42815.324
300.29980.4904-0.2661.78920.27221.510.39630.6759-0.4117-0.5713-0.20660.45180.44660.1996-0.17490.6170.2399-0.21260.811-0.19450.476120.75945.897-4.752
314.1755-0.14370.49735.5509-0.52944.04260.26510.07290.215-0.3453-0.52940.50670.0543-0.25980.30290.51690.0795-0.16170.6725-0.14380.345416.27157.903-1.676
320.9612-0.9320.04651.9452-0.79831.3372-0.2069-0.89250.01790.14870.06520.5034-0.0841-0.49030.09910.19510.089-0.06130.8266-0.28530.5209-0.80374.3568.595
332.1237-0.99470.17552.1003-0.49230.7101-0.194-0.55010.71910.2465-0.01250.3611-0.2316-0.44480.05080.30620.111-0.0930.8466-0.31890.6764-2.22576.7771.445
345.15631.7419-0.3554.33560.07274.4389-0.38160.0924-0.6326-0.2126-0.0174-0.6457-0.47410.70790.37550.388-0.1585-0.1710.7038-0.00970.747429.83580.686-5.056
351.07370.24130.44423.39490.73522.6318-0.3933-0.1854-0.03870.56670.29210.16160.03210.52640.10760.64790.26490.00330.46970.08280.218612.98642.3-34.705
363.1102-1.7722-0.15894.24150.11543.1366-0.4015-0.5684-0.95980.79240.32450.32160.96130.32860.09420.94610.33080.17310.54320.12220.641517.8727.21-37.401
373.3555-2.0645-0.43663.69952.44553.6627-0.4966-0.4346-0.57310.46240.19350.57710.1078-0.17170.30390.69550.21430.12590.46430.07520.39697.23443.843-30.236
383.5899-1.147-1.91153.25351.3114.6057-0.62750.0337-0.50891.0768-0.40181.63370.4138-0.35830.84640.8050.12530.29110.5174-0.01970.8545-0.15741.144-29.238
393.74040.6383-1.18742.88021.41183.162-0.3672-0.7162-0.62550.9513-0.04061.39380.1938-0.70150.36010.84030.05530.33260.79680.06341.2665-17.49951.015-15.215
400.7640.7962-0.6497.34133.20393.0764-0.7584-0.02750.1322-0.24760.45410.90110.34-0.01950.27340.49660.0456-0.01850.65160.07330.8347-13.21756.627-21.16
411.0829-0.24690.54150.4629-0.83963.5838-0.2685-0.1430.3750.0930.04720.075-1.0790.3557-0.05751.3250.2092-0.30690.5732-0.02420.217313.55667.179-34.356
421.0908-1.41571.06321.8367-1.37891.0398-0.335-0.62431.52970.51750.2221-0.0418-1.073-0.1922-0.08951.77480.0586-0.19020.7665-0.02191.202611.11989.085-30.638
436.6271-0.3123-0.06750.01780.07081.3032-1.2212-1.14931.18160.50580.3726-0.1198-1.03950.61240.75991.6124-0.0557-0.35231.0502-0.07780.720623.14778.237-31.996
443.64450.1123-0.71932.7640.41531.1241-0.26640.77380.39040.25340.053-0.1224-1.18540.46010.1531.1284-0.1328-0.14540.63060.0040.264815.8566.227-43.773
450.68340.2252-0.11590.8751-0.73760.633-0.6973-0.22890.46890.15480.22330.4054-0.753-0.3087-0.02121.44650.3785-0.30710.50640.05510.50192.43765.389-35.824
466.82451.39642.04573.9934-3.43744.6229-0.4132-0.4630.36240.0841-0.289-0.0401-0.4507-0.28560.84241.11370.1134-0.18070.6090.07540.44048.43364.416-36.644
472.414-1.05540.12064.65570.60360.1061-0.9913-0.58920.37880.48090.39180.3842-0.3814-0.3394-0.21761.59250.4597-0.22060.5685-0.08880.54745.50572.326-38.685
480.2474-0.69660.05013.3383-0.42150.3256-0.4507-0.31410.39930.40840.050.2984-0.4511-0.0385-0.31691.53410.5391-0.49060.6531-0.08630.9696-2.77478.902-39.629
499.6814-3.6759-1.08523.0369-1.42552.1816-1.0880.1273-1.9576-0.54810.57112.0320.9094-0.46460.35111.1320.1293-0.14840.5891-0.16331.1819-15.92251.785-51.771
501.13270.53180.12533.43240.22741.1215-0.3510.10120.85130.67560.1061.0063-0.6678-0.39410.32481.11420.2844-0.29390.6425-0.07411.4044-16.92266.523-54.288
511.4891-0.23120.68020.0373-0.1060.3102-0.08290.27820.12790.22910.03281.6557-0.7098-0.60.07690.59320.19450.01960.6510.07931.3179-14.00455.227-56.28
522.5314-1.9271-0.38783.42360.23811.3057-0.4704-0.48590.17850.93370.5550.5197-0.2289-0.3554-0.02160.55280.18060.030.46180.05120.6953-7.99651.328-47.407
535.03031.1794-0.34312.0265-0.89792.3872-0.22070.27150.0663-0.2650.22340.48560.0121-0.1908-0.01420.1901-0.0841-0.1590.23920.05040.57990.67833.53-75.421
541.1877-1.19711.85893.13040.59016.0886-0.42070.2870.49120.1686-0.02670.8572-0.1336-0.76050.45220.2852-0.1239-0.00260.81410.04990.8932-16.15731.84-65.085
552.79380.75470.78371.66880.69461.4291-0.43810.43980.469-0.46090.17790.3355-0.3023-0.12470.23240.2778-0.2265-0.18550.53930.08610.9908-11.04430.877-79.044
561.936-0.26371.70350.0465-0.0074.9373-0.19990.5156-0.0847-0.33630.10170.27410.40770.07820.09920.2411-0.1859-0.08870.2713-0.02090.63911.3523.998-76.786
572.88130.20831.18692.1324-0.13283.0818-0.09910.217-0.2615-0.2010.16060.5265-0.0023-0.1587-0.0550.0988-0.0583-0.05450.19850.01870.29719.29834.252-71.447
582.1428-0.4584-0.2321.80531.15823.8649-0.162-0.0775-0.31360.11920.30390.27040.31820.1444-0.13060.1699-0.054-0.08560.27910.01140.46924.54530.595-66.795
591.7475-1.1191-1.09621.08790.67891.6185-0.1038-0.81870.13070.0250.27840.26560.2658-0.2009-0.13680.1253-0.0291-0.0170.44140.07980.4585.39531.675-56.527
602.8193-1.4582-0.93743.30670.90373.5952-0.4852-0.6417-0.28890.33820.1942-0.43710.13080.62910.30050.22030.07810.0240.38340.03780.406633.17427.542-59.027
615.1309-1.2358-0.24562.8208-0.83276.02930.0180.3655-0.0738-0.02980.0981-0.0012-0.06440.2381-0.08590.142-0.02870.06560.2377-0.05470.448931.95328.059-65.171
622.02470.8758-1.05572.3482-1.11383.93780.07640.1286-0.0189-0.4417-0.02840.09661.1026-0.1648-0.02470.4915-0.0514-0.07880.26930.0260.249721.21138.17-92.7
631.69161.00650.13023.24190.41544.9329-0.09310.3801-0.1949-0.81770.1668-0.27120.72460.3762-0.06720.82350.0484-0.01870.36120.06750.253726.20240.329-102.613
643.01832.6868-0.51714.31280.67445.7989-0.073-0.0834-0.0472-0.275-0.0062-0.2210.30760.29660.04630.25620.0774-0.05880.25970.030.195624.92243.06-86.389
650.5430.82091.20332.51890.49764.11680.1467-0.2229-0.18780.211-0.10260.0034-0.11681.0149-0.03050.3041-0.16030.00410.2370.03250.368629.22451.992-78.066
662.14730.58581.16783.5945-0.09190.68080.2831-0.3260.74520.9197-0.25710.1401-0.0418-0.03570.06310.6142-0.15680.09320.3067-0.01360.440625.73963.026-60.619
673.5659-0.51850.57134.37530.05713.20750.1222-0.14440.51390.6146-0.30150.4475-0.0993-0.35610.17340.4827-0.16550.0730.2369-0.00020.431521.18862.571-66.466
684.89560.22960.33433.62760.1293.75530.0978-0.5371-0.50690.95-0.23730.57140.4813-0.69260.1640.5239-0.16180.08340.3029-0.01290.397519.54950.403-66.144
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:91 )A1 - 91
2X-RAY DIFFRACTION2( CHAIN A AND RESID 92:180 )A92 - 180
3X-RAY DIFFRACTION3( CHAIN A AND RESID 181:236 )A181 - 236
4X-RAY DIFFRACTION4( CHAIN A AND RESID 237:302 )A237 - 302
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:42 )B1 - 42
6X-RAY DIFFRACTION6( CHAIN B AND RESID 43:65 )B43 - 65
7X-RAY DIFFRACTION7( CHAIN B AND RESID 66:200 )B66 - 200
8X-RAY DIFFRACTION8( CHAIN B AND RESID 201:226 )B201 - 226
9X-RAY DIFFRACTION9( CHAIN B AND RESID 227:302 )B227 - 302
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1:43 )C1 - 43
11X-RAY DIFFRACTION11( CHAIN C AND RESID 44:70 )C44 - 70
12X-RAY DIFFRACTION12( CHAIN C AND RESID 71:180 )C71 - 180
13X-RAY DIFFRACTION13( CHAIN C AND RESID 181:236 )C181 - 236
14X-RAY DIFFRACTION14( CHAIN C AND RESID 237:273 )C237 - 273
15X-RAY DIFFRACTION15( CHAIN C AND RESID 274:303 )C274 - 303
16X-RAY DIFFRACTION16( CHAIN D AND RESID 1:200 )D1 - 200
17X-RAY DIFFRACTION17( CHAIN D AND RESID 201:303 )D201 - 303
18X-RAY DIFFRACTION18( CHAIN E AND RESID 1:70 )E1 - 70
19X-RAY DIFFRACTION19( CHAIN E AND RESID 71:200 )E71 - 200
20X-RAY DIFFRACTION20( CHAIN E AND RESID 201:303 )E201 - 303
21X-RAY DIFFRACTION21( CHAIN F AND RESID 1:70 )F1 - 70
22X-RAY DIFFRACTION22( CHAIN F AND RESID 71:200 )F71 - 200
23X-RAY DIFFRACTION23( CHAIN F AND RESID 201:226 )F201 - 226
24X-RAY DIFFRACTION24( CHAIN F AND RESID 227:302 )F227 - 302
25X-RAY DIFFRACTION25( CHAIN G AND RESID 1:42 )G1 - 42
26X-RAY DIFFRACTION26( CHAIN G AND RESID 43:99 )G43 - 99
27X-RAY DIFFRACTION27( CHAIN G AND RESID 100:139 )G100 - 139
28X-RAY DIFFRACTION28( CHAIN G AND RESID 140:155 )G140 - 155
29X-RAY DIFFRACTION29( CHAIN G AND RESID 156:213 )G156 - 213
30X-RAY DIFFRACTION30( CHAIN G AND RESID 214:274 )G214 - 274
31X-RAY DIFFRACTION31( CHAIN G AND RESID 275:302 )G275 - 302
32X-RAY DIFFRACTION32( CHAIN H AND RESID 1:43 )H1 - 43
33X-RAY DIFFRACTION33( CHAIN H AND RESID 44:200 )H44 - 200
34X-RAY DIFFRACTION34( CHAIN H AND RESID 201:302 )H201 - 302
35X-RAY DIFFRACTION35( CHAIN I AND RESID 1:43 )I1 - 43
36X-RAY DIFFRACTION36( CHAIN I AND RESID 44:91 )I44 - 91
37X-RAY DIFFRACTION37( CHAIN I AND RESID 92:139 )I92 - 139
38X-RAY DIFFRACTION38( CHAIN I AND RESID 140:214 )I140 - 214
39X-RAY DIFFRACTION39( CHAIN I AND RESID 215:260 )I215 - 260
40X-RAY DIFFRACTION40( CHAIN I AND RESID 261:306 )I261 - 306
41X-RAY DIFFRACTION41( CHAIN J AND RESID 1:43 )J1 - 43
42X-RAY DIFFRACTION42( CHAIN J AND RESID 44:59 )J44 - 59
43X-RAY DIFFRACTION43( CHAIN J AND RESID 60:91 )J60 - 91
44X-RAY DIFFRACTION44( CHAIN J AND RESID 92:110 )J92 - 110
45X-RAY DIFFRACTION45( CHAIN J AND RESID 111:139 )J111 - 139
46X-RAY DIFFRACTION46( CHAIN J AND RESID 140:155 )J140 - 155
47X-RAY DIFFRACTION47( CHAIN J AND RESID 156:180 )J156 - 180
48X-RAY DIFFRACTION48( CHAIN J AND RESID 181:200 )J181 - 200
49X-RAY DIFFRACTION49( CHAIN J AND RESID 201:226 )J201 - 226
50X-RAY DIFFRACTION50( CHAIN J AND RESID 227:245 )J227 - 245
51X-RAY DIFFRACTION51( CHAIN J AND RESID 246:273 )J246 - 273
52X-RAY DIFFRACTION52( CHAIN J AND RESID 274:306 )J274 - 306
53X-RAY DIFFRACTION53( CHAIN K AND RESID 1:48 )K1 - 48
54X-RAY DIFFRACTION54( CHAIN K AND RESID 49:65 )K49 - 65
55X-RAY DIFFRACTION55( CHAIN K AND RESID 66:84 )K66 - 84
56X-RAY DIFFRACTION56( CHAIN K AND RESID 85:110 )K85 - 110
57X-RAY DIFFRACTION57( CHAIN K AND RESID 111:155 )K111 - 155
58X-RAY DIFFRACTION58( CHAIN K AND RESID 156:180 )K156 - 180
59X-RAY DIFFRACTION59( CHAIN K AND RESID 181:200 )K181 - 200
60X-RAY DIFFRACTION60( CHAIN K AND RESID 201:243 )K201 - 243
61X-RAY DIFFRACTION61( CHAIN K AND RESID 244:303 )K244 - 303
62X-RAY DIFFRACTION62( CHAIN L AND RESID 1:43 )L1 - 43
63X-RAY DIFFRACTION63( CHAIN L AND RESID 44:110 )L44 - 110
64X-RAY DIFFRACTION64( CHAIN L AND RESID 111:180 )L111 - 180
65X-RAY DIFFRACTION65( CHAIN L AND RESID 181:214 )L181 - 214
66X-RAY DIFFRACTION66( CHAIN L AND RESID 215:237 )L215 - 237
67X-RAY DIFFRACTION67( CHAIN L AND RESID 238:273 )L238 - 273
68X-RAY DIFFRACTION68( CHAIN L AND RESID 274:302 )L274 - 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://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