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- PDB-7kf4: Crystal structure from SARS-CoV-2 NendoU NSP15 -

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基本情報

登録情報
データベース: PDB / ID: 7kf4
タイトルCrystal structure from SARS-CoV-2 NendoU NSP15
要素Uridylate-specific endoribonuclease
キーワードVIRAL PROTEIN / HYDROLASE / NSP15 / NendoU / covid-19 / covid / sars / sars-cov-2 / endoribonuclease
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
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 / : ...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 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
類似検索 - ドメイン・相同性
CITRIC ACID / 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: 2.61 Å
データ登録者Godoy, A.S. / Nakamura, A.M. / Pereira, H.M. / Noske, G.D. / Gawriljuk, V.O. / Fernandes, R.S. / Oliveira, K.I.Z. / Oliva, G.
資金援助 ブラジル, 1件
組織認可番号国
Sao Paulo Research Foundation (FAPESP)2013/07600-3 ブラジル
引用ジャーナル: Nucleic Acids Res / 年: 2023
タイトル: Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.
著者: Andre Schutzer Godoy / Aline Minalli Nakamura / Alice Douangamath / Yun Song / Gabriela Dias Noske / Victor Oliveira Gawriljuk / Rafaela Sachetto Fernandes / Humberto D Muniz Pereira / ...著者: Andre Schutzer Godoy / Aline Minalli Nakamura / Alice Douangamath / Yun Song / Gabriela Dias Noske / Victor Oliveira Gawriljuk / Rafaela Sachetto Fernandes / Humberto D Muniz Pereira / Ketllyn Irene Zagato Oliveira / Daren Fearon / Alexandre Dias / Tobias Krojer / Michael Fairhead / Alisa Powell / Louise Dunnet / Jose Brandao-Neto / Rachael Skyner / Rod Chalk / Dávid Bajusz / Miklós Bege / Anikó Borbás / György Miklós Keserű / Frank von Delft / Glaucius Oliva /
要旨: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and plays a critical role in the ability of the virus to evade the immune system. NendoU is a promising target for the development of new antiviral drugs. However, the complexity of the enzyme's structure and kinetics, along with the broad range of recognition sequences and lack of structural complexes, hampers the development of inhibitors. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index, and with no influence of manganese on enzymatic activity. Through combining cryo-electron microscopy at different pHs, X-ray crystallography and biochemical and structural analysis, we showed that NendoU can shift between open and closed forms, which probably correspond to active and inactive states, respectively. We also explored the possibility of NendoU assembling into larger supramolecular structures and proposed a mechanism for allosteric regulation. In addition, we conducted a large fragment screening campaign against NendoU and identified several new allosteric sites that could be targeted for the development of new inhibitors. Overall, our findings provide insights into the complex structure and function of NendoU and offer new opportunities for the development of inhibitors.
履歴
登録2020年10月13日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年12月2日Provider: repository / タイプ: Initial release
改定 1.12023年5月10日Group: Database references / カテゴリ: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22023年10月25日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 1.32024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
C: Uridylate-specific endoribonuclease
D: Uridylate-specific endoribonuclease
E: Uridylate-specific endoribonuclease
F: Uridylate-specific endoribonuclease
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)235,82812
ポリマ－234,6756
非ポリマー1,1536
水7,728429
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: native gel electrophoresis
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area20690 Å2
ΔGint-104 kcal/mol
Surface area84910 Å2
手法PISA
単位格子
Length a, b, c (Å)85.125, 151.163, 199.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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要素

#1: タンパク質
Uridylate-specific endoribonuclease / NSP15 / NendoU


分子量: 39112.535 Da / 分子数: 6 / 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, 加水分解酵素; エステル加水分解酵素
#2: 化合物
ChemComp-CIT / CITRIC ACID / クエン酸


分子量: 192.124 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C6H8O7
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 429 / 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
Has protein modificationY

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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: 2.74 Å3/Da / 溶媒含有率: 55.05 %
結晶化温度: 293 K / 手法: 蒸気拡散法 / pH: 5 / 詳細: 0.1 M trisodium citrate pH 5, 14 % w/v PEG6000

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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: MAX IV / ビームライン: BioMAX / 波長: 0.976254 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2020年6月13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: 0.976254 Å / 相対比: 1
反射解像度: 2.61→49.16 Å / Num. obs: 78886 / % possible obs: 99.73 % / 冗長度: 13.8 % / CC1/2: 0.998 / Net I/σ(I): 8.24
反射 シェル解像度: 2.61→2.703 Å / Num. unique obs: 7756 / CC1/2: 0.527

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解析

ソフトウェア
名称バージョン分類
BUSTER2.10.3精密化
PDB_EXTRACT3.25データ抽出
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: 6x1b

6x1b


解像度: 2.61→49.16 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.915 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.717 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.712 / SU Rfree Blow DPI: 0.293 / SU Rfree Cruickshank DPI: 0.298
Rfactor反射数%反射Selection details
Rfree0.246 4004 5.09 %RANDOM
Rwork0.219 ---
obs0.22 78707 99.8 %-
原子変位パラメータBiso max: 282.46 Å2 / Biso mean: 74.07 Å2 / Biso min: 25.11 Å2
Baniso -1Baniso -2Baniso -3
1--27.3512 Å20 Å20 Å2
2--17.6677 Å20 Å2
3---9.6835 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
精密化ステップサイクル: final / 解像度: 2.61→49.16 Å
タンパク質核酸リガンド溶媒全体
原子数16447 0 78 429 16954
Biso mean--108.38 57.7 -
残基数----2088
拘束条件
Refine-IDタイプ数Restraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5856SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes469HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2412HARMONIC5
X-RAY DIFFRACTIONt_it16897HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2226SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact19009SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16897HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg22946HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion19.7
LS精密化 シェル解像度: 2.61→2.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.303 298 5.21 %
Rwork0.266 5423 -
all0.268 5721 -
obs--99.69 %
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00070.49360.04570.00041.42350.00260.1213-0.1053-0.1407-0.0469-0.1399-0.07490.3616-0.09280.01860.3273-0.04880.01040.2980.01170.3666.819746.625835.4651
20.1308-0.16591.06751.70941.23412.1755-0.04250.04780.22620.05210.0261-0.0676-0.0712-0.18380.01640.27930.0096-0.02810.2412-0.01980.392715.944767.90426.9555
31.4538-1.1410.48171.0101-0.38590.79650.30990.31320.1801-0.3723-0.3235-0.2990.28880.20420.01360.59720.13370.17570.49340.16480.423737.368457.64768.4215
40.0416-0.612-1.48990.24710.77760.63220.04460.2520.1614-0.1344-0.0326-0.25050.10610.113-0.01190.43540.08060.0970.45420.08410.583342.336561.878816.2166
52.01761.93951.94342.21922.34172.2385-1.1757-0.633.1517-4.4371-1.99970.8413-5.4473-3.48263.17540.50710.07720.75491.0198-0.33741.071745.655461.470726.3093
60.58450.4495-0.60671.0639-2.130200.08140.0129-0.0558-0.0547-0.1445-0.00330.2322-0.05830.06310.36380.02940.05110.3621-0.0110.387836.684546.571255.3226
70.22020.60260.55242.1698-1.26782.0557-0.01810.00520.08260.1070.01310.1621-0.06750.07280.0050.36170.005-0.06470.2582-0.02440.437227.551467.939863.7281
81.31530.5401-0.48770.511-1.09190.28920.1029-0.19740.04880.3082-0.06320.14560.0985-0.0922-0.03970.5496-0.06230.02260.4364-0.04770.39176.470857.409680.6584
90.06461.124-0.23690.04010.28980.34980.0078-0.10640.05490.13340.0784-0.07620.0522-0.1231-0.08630.4247-0.02990.08190.4073-0.06790.5297-0.20262.560575.6244
101.99631.98221.99872.01311.95412.028-0.4983-0.03490.46831.0826-0.3542-1.2449-1.3725-0.22990.85260.64170.33370.06311.15030.20050.8712-2.61261.764263.49
110.0039-0.16760.4381.0814-0.5060-0.17730.08370.05420.01380.1431-0.0480.0393-0.06410.03420.6885-0.02580.03360.39140.04120.37423.555320.797337.0657
120.54841.0421-0.8840.01370.37641.5460.02630.0048-0.1481-0.0329-0.02420.06190.08090.0031-0.00220.7584-0.04740.01870.2232-0.00070.44671.989917.145725.6717
130.2376-0.34110.0430.7073-0.12870.35130.09110.0924-0.01040.034-0.0910.01040.2097-0.0253-0.00010.6081-0.1105-0.0690.4819-0.01390.3516-0.487740.61618.5154
149.0345-8.8894-5.87249.14517.28829.6051-0.21680.0557-0.7543-0.04790.1524-0.2024-0.007-0.44440.06430.71830.24560.11720.81630.03991.1155-7.79846.484422.3961
150.0104-0.0340.24230.3907-0.56810.5484-0.207-0.09020.0191-0.01380.13840.16430.155-0.03470.06860.66550.00310.04970.42180.00170.466420.084120.730453.6662
160.4551-0.7303-0.16980.0627-0.14761.6992-0.1274-0.0506-0.253-0.08360.125-0.108-0.1162-0.01150.00240.42670.01210.15580.28020.02810.405541.515717.161965.1775
170-0.8932-0.39252.25390.80860-0.1813-0.11390.00650.14660.1696-0.1172-0.0880.16840.01170.55790.1614-0.05540.5076-0.04730.35940.104639.071183.6929
180.4346-0.2938-0.90060.0010.41510.4198-0.0158-0.08430.1461-0.02970.011-0.13140.1187-0.12470.00480.48060.1463-0.00530.4759-0.05780.453948.723942.531680.4701
192.0679-3.38672.11582.0372-2.73392.11460.9532-1.55461.4-0.6349-0.824-2.18860.4084-3.5272-0.12921.21540.05510.08010.9758-0.24690.531349.444145.305869.5477
200-0.4432-0.45060.4834-0.02760.46130.0044-0.01110.1177-0.0405-0.0143-0.1079-0.1293-0.01790.00990.3648-0.02030.02620.40970.03680.41444.587751.561652.2398
210.3891-0.1125-0.79910.3546-0.76960.9757-0.0019-0.0395-0.0017-0.17570.023-0.03090.359-0.0985-0.02110.4343-0.1514-0.0140.35970.01060.3356-6.13232.258358.9963
220.08860.06721.35760.0106-0.4470.0097-0.0487-0.51320.4194-0.1751-0.0150.25460.2892-0.24180.06370.6812-0.16940.03020.49330.0140.5306-4.966220.95970.9219
231.8724-0.23260.20530.69510.34550.6671-0.0825-0.202-0.1496-0.0220.06170.00960.31630.20480.02080.505-0.01670.0670.46260.030.379911.259717.806583.5372
2400.6570.29580.05630.77390.00020.06-0.12260.0122-0.2504-0.01740.00440.2166-0.0488-0.04260.5325-0.07080.05880.5062-0.00090.48327.541112.453676.2867
250.40630.36340.30780.57240.14960.10620.10880.2008-0.2696-0.1616-0.1719-0.17870.0454-0.07730.06310.6845-0.07130.02930.51430.010.5317.14164.079475.831
261.99341.99732.00181.99742.00411.99130.8149-2.1481-0.84383.71860.8111-2.99834.74322.649-1.6260.88270.49440.05880.77160.62681.343910.99459.240165.8591
270.8066-0.5611-0.79880.1063-0.64841.1705-0.02940.11110.00320.1950.02040.00720.20440.05860.0090.33560.03720.06110.35590.06350.426237.373848.276938.3603
280.7146-1.2890.03590.60520.66470.06130.1095-0.0065-0.0161-0.2003-0.0731-0.11050.39020.0632-0.03640.50530.16770.14480.33760.10330.329152.715330.610130.6557
291.2717-1.20010.3470.096-0.15870.00720.24660.3227-0.229-0.1393-0.21730.04890.83220.1183-0.02921.10660.26410.15110.58660.04770.404236.055316.896211.8043
300.85550.06451.34060.2073-0.16950.3860.1318-0.6054-0.7099-0.2475-0.0521-0.25021.7887-0.2589-0.07971.2765-0.0202-0.07430.64-0.08350.625136.84274.613715.1956
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|0 - B|60 }B0 - 60
2X-RAY DIFFRACTION2{ B|61 - B|183 }B61 - 183
3X-RAY DIFFRACTION3{ B|184 - B|267 }B184 - 267
4X-RAY DIFFRACTION4{ B|268 - B|345 }B268 - 345
5X-RAY DIFFRACTION5{ B|346 - B|346 }B346
6X-RAY DIFFRACTION6{ A|0 - A|60 }A0 - 60
7X-RAY DIFFRACTION7{ A|61 - A|183 }A61 - 183
8X-RAY DIFFRACTION8{ A|184 - A|276 }A184 - 276
9X-RAY DIFFRACTION9{ A|277 - A|345 }A277 - 345
10X-RAY DIFFRACTION10{ A|346 - A|346 }A346
11X-RAY DIFFRACTION11{ C|0 - C|60 }C0 - 60
12X-RAY DIFFRACTION12{ C|61 - C|183 }C61 - 183
13X-RAY DIFFRACTION13{ C|184 - C|345 }C184 - 345
14X-RAY DIFFRACTION14{ C|346 - C|346 }C346
15X-RAY DIFFRACTION15{ D|0 - D|60 }D0 - 60
16X-RAY DIFFRACTION16{ D|61 - D|183 }D61 - 183
17X-RAY DIFFRACTION17{ D|184 - D|276 }D184 - 276
18X-RAY DIFFRACTION18{ D|277 - D|345 }D277 - 345
19X-RAY DIFFRACTION19{ D|346 - D|346 }D346
20X-RAY DIFFRACTION20{ E|0 - E|38 }E0 - 38
21X-RAY DIFFRACTION21{ E|39 - E|183 }E39 - 183
22X-RAY DIFFRACTION22{ E|184 - E|203 }E184 - 203
23X-RAY DIFFRACTION23{ E|204 - E|276 }E204 - 276
24X-RAY DIFFRACTION24{ E|277 - E|325 }E277 - 325
25X-RAY DIFFRACTION25{ E|326 - E|345 }E326 - 345
26X-RAY DIFFRACTION26{ E|346 - E|346 }E346
27X-RAY DIFFRACTION27{ F|0 - F|60 }F0 - 60
28X-RAY DIFFRACTION28{ F|61 - F|183 }F61 - 183
29X-RAY DIFFRACTION29{ F|184 - F|325 }F184 - 325
30X-RAY DIFFRACTION30{ F|326 - F|345 }F326 - 345

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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