登録情報 | データベース: PDB / ID: 6yva |
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タイトル | PLpro-C111S with mISG15 |
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要素 | - Replicase polyprotein 1a
- Ubiquitin-like protein ISG15
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キーワード | CELL INVASION / Deubiquitinase / papain-like-protease / SARS-CoV-2 / ISG15 / complex |
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機能・相同性 | 機能・相同性情報
positive regulation of protein oligomerization / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication ...positive regulation of protein oligomerization / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / viral genome replication / positive regulation of erythrocyte differentiation / methyltransferase activity / integrin-mediated signaling pathway / response to bacterium / response to virus / modification-dependent protein catabolic process / protein tag activity / positive regulation of type II interferon production / integrin binding / 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 / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 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 / DNA helicase / endonuclease activity / methylation / defense response to virus / 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 / defense response to bacterium / 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 / ubiquitin protein ligase binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / extracellular region / ATP binding / membrane / cytoplasm類似検索 - 分子機能 Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / : / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / RNA-dependent RNA polymerase, SARS-CoV-like / Ubiquitin family / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : ...Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / : / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / RNA-dependent RNA polymerase, SARS-CoV-like / Ubiquitin family / 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 / Ubiquitin homologues / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Lipocalin signature. / Ubiquitin domain profile. / Ubiquitin-like 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 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類似検索 - ドメイン・相同性 Replicase polyprotein 1a / Replicase polyprotein 1ab / Ubiquitin-like protein ISG15類似検索 - 構成要素 |
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生物種 | ![](img/tx_virus.gif) Severe acute respiratory syndrome coronavirus 2 (ウイルス)
![](img/tx_mammal.gif) Mus musculus (ハツカネズミ) |
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手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3.18 Å |
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データ登録者 | Shin, D. / Dikic, I. |
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資金援助 | ドイツ, 1件 組織 | 認可番号 | 国 |
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German Research Foundation (DFG) | SFB1177 | ドイツ |
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引用 | ジャーナル: Nature / 年: 2020タイトル: Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. 著者: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / Wilhelm, A. / van der Heden van ...著者: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / Wilhelm, A. / van der Heden van Noort, G.J. / Ovaa, H. / Muller, S. / Knobeloch, K.P. / Rajalingam, K. / Schulman, B.A. / Cinatl, J. / Hummer, G. / Ciesek, S. / Dikic, I.#1: ジャーナル: Nature / 年: 2020タイトル: Inhibition of papain-like protease PLpro blocks SARS-CoV-2 spread and promotes anti-viral immunity 著者: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / van der Heden van Noort, G.J. / ...著者: Shin, D. / Mukherjee, R. / Grewe, D. / Bojkova, D. / Baek, K. / Bhattacharya, A. / Schulz, L. / Widera, M. / Mehdipour, A.R. / Tascher, G. / Geurink, P.P. / van der Heden van Noort, G.J. / Ovaa, H. / Knobeloch, K.P. / Rajalingam, K. / Schulman, B.A. / Cinatl, J. / Hummer, G. / Ciesek, S. / Dikic, I. |
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履歴 | 登録 | 2020年4月28日 | 登録サイト: PDBE / 処理サイト: PDBE |
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改定 1.0 | 2020年5月13日 | Provider: repository / タイプ: Initial release |
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改定 2.0 | 2020年7月15日 | Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / struct_asym / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns.B_iso_Wilson_estimate / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id 解説: Real space R-factor 詳細: We have refined the structure to have a better R-free value. Provider: author / タイプ: Coordinate replacement |
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改定 2.1 | 2020年8月12日 | Group: Database references / カテゴリ: citation / citation_author |
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改定 2.2 | 2020年12月9日 | Group: Database references / カテゴリ: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID |
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改定 2.3 | 2021年8月11日 | Group: Database references / カテゴリ: citation / 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_PubMed / _database_2.pdbx_DOI / _database_2.pdbx_database_accession |
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改定 2.4 | 2024年1月24日 | Group: Data collection / Refinement description カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model |
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