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- PDB-9fwn: Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex wit... -

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データベース: PDB / ID: 9fwn
タイトルCrystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00219
要素
  • Guanine-N7 methyltransferase nsp14
  • Non-structural protein 10
キーワードVIRAL PROTEIN / exoribonuclease / nsp10 / nsp14 / fragment screen
機能・相同性
機能・相同性情報


viral genome replication / methyltransferase activity / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素（リアーゼ）; P-Oリアーゼ類; - / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins ...viral genome replication / methyltransferase activity / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素（リアーゼ）; P-Oリアーゼ類; - / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / 3'-5'-RNA exonuclease activity / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / host cell endosome / single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / symbiont-mediated degradation of host mRNA / forked DNA-dependent helicase activity / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / four-way junction helicase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / endonuclease activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / single-stranded RNA binding / host cell perinuclear region of cytoplasm / regulation of autophagy / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / 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
: / Replicase polyprotein 1a / 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 / フーリエ合成 / 解像度: 1.866 Å
データ登録者Krojer, T. / Kozielski, F. / Sele, C. / Nyblom, M. / Fisher, S.Z. / Knecht, W.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: To Be Published
タイトル: Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00219
著者: Krojer, T. / Kozielski, F. / Sele, C. / Nyblom, M. / Fisher, S.Z. / Knecht, W.
履歴
登録2024年6月30日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02025年7月9日Provider: repository / タイプ: Initial release

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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: Non-structural protein 10
B: Guanine-N7 methyltransferase nsp14
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)47,11210
ポリマ－46,5602
非ポリマー5538
水3,333185
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: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-40 kcal/mol
Surface area18200 Å2
手法PISA
単位格子
Length a, b, c (Å)61.464, 70.503, 108.617
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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要素

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タンパク質 , 2種, 2分子 AB

#1: タンパク質 Non-structural protein 10 / nsp10 / Growth factor-like peptide / GFL


分子量: 13805.737 Da / 分子数: 1 / 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)
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0DTC1
#2: タンパク質 Guanine-N7 methyltransferase nsp14 / Non-structural protein 14 / nsp14 / Proofreading exoribonuclease nsp14 / ExoN


分子量: 32753.783 Da / 分子数: 1 / 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, mRNA (guanine-N7)-methyltransferase, 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

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非ポリマー , 5種, 193分子

#3: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn
#4: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
#5: 化合物 ChemComp-A1IGN / 1-methyl-1-(phenylmethyl)urea


分子量: 164.204 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C9H12N2O / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物 ChemComp-DMS / DIMETHYL SULFOXIDE / 2-チアプロパン2-オキシド


分子量: 78.133 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H6OS / コメント: DMSO, 沈殿剤*YM
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 185 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationN

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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: 2.53 Å3/Da / 溶媒含有率: 51.33 %
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: Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 30.50%w/v Morpheus Amino acids: 0.20M

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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: 0.97625 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年7月9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: 0.97625 Å / 相対比: 1
反射解像度: 1.866→59.137 Å / Num. obs: 39604 / % possible obs: 99 % / 冗長度: 13.39 %
詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.998 / CC1/2 anomalous: -0.126 / Rmerge(I) obs: 0.1137 / Rpim(I) all: 0.0322 / Rrim(I) all: 0.1183 / AbsDiff over sigma anomalous: 0.832 / Net I/σ(I): 14.64 / Num. measured all: 530102 / % possible anomalous: 98.9 / Redundancy anomalous: 7.07
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
5.063-59.13712.450.051939.472702427024217121710.998-0.0050.01520.05411.2271007.1999.9
4.019-5.06313.170.050139.152715227152206120610.997-0.1980.01420.05210.9251007.2100
3.511-4.01912.970.059334.762563325633197719770.997-0.1440.01690.06170.88297.16.9897.2
3.19-3.51112.970.081227.912424624246186918690.995-0.2460.02340.08450.904926.9692.5
2.961-3.1913.430.097924.022712527125202020200.995-0.2290.02770.10180.871007.11100
2.787-2.96113.60.123320.272708227082199219920.993-0.1410.03480.12820.8981007.18100
2.647-2.78713.310.155116.42392323923179817980.99-0.1770.04360.16130.84689.27.0789.7
2.532-2.64713.860.1814.622764127641199419940.989-0.1850.050.1870.8621007.28100
2.434-2.53213.920.226312.372780827808199819980.988-0.0830.06280.2350.8171007.31100
2.35-2.43413.430.271610.492628726287195719570.981-0.0910.07660.28240.8081007.03100
2.277-2.3513.030.32668.972579225792197919790.977-0.0350.09370.340.791006.8100
2.212-2.27713.360.39817.762687926879201220120.973-0.0020.11270.41410.791007.01100
2.154-2.21213.560.44497.172703227032199419940.9670.0230.12490.46240.8181007.08100
2.101-2.15413.460.54395.922653026530197119710.963-0.0450.1530.56530.771007.02100
2.053-2.10113.480.68554.952642826428196019600.938-0.010.19240.71240.8091007.02100
2.01-2.05313.450.8274.122680226802199319930.909-0.0250.23230.85950.7431007.03100
1.969-2.0113.540.91943.612659926599196419640.901-0.0180.25760.95530.7471007.04100
1.932-1.96913.561.125932671726717197019700.857-0.0460.31491.16980.7511007.05100
1.898-1.93213.561.28412.642680826808197719770.839-0.0490.35941.33420.7481007.05100
1.866-1.89813.661.53482.152659426594194719470.766-0.0620.42781.59430.6931007.07100

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解析

ソフトウェア
名称バージョン分類
autoPROCdata processing
XDSJan 10, 2022データ削減
Aimless0.7.7データスケーリング
TRUNCATE7.1.015data processing
BUSTER2.10.4精密化
精密化構造決定の手法: フーリエ合成 / 解像度: 1.866→35.25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.14 / 交差検証法: THROUGHOUT / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.126
Rfactor反射数%反射Selection details
Rfree0.2307 2025 -RANDOM
Rwork0.2064 ---
obs0.2076 39598 99 %-
原子変位パラメータBiso mean: 33.19 Å2
Baniso -1Baniso -2Baniso -3
1--10.2847 Å20 Å20 Å2
2--3.6577 Å20 Å2
3---6.627 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
精密化ステップサイクル: LAST / 解像度: 1.866→35.25 Å
タンパク質核酸リガンド溶媒全体
原子数3192 0 22 185 3399
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083322HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.984523HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1108SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes564HARMONIC5
X-RAY DIFFRACTIONt_it3322HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion443SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2908SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.67
X-RAY DIFFRACTIONt_other_torsion15.86
LS精密化 シェル解像度: 1.87→1.88 Å
Rfactor反射数%反射
Rfree0.2369 32 -
Rwork0.2753 --
obs0.2737 792 100 %

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  • 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

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