Entry Database : PDB / ID : 7mhl Structure visualization Downloads & linksTitle Ensemble refinement structure of SARS-CoV-2 main protease (Mpro) at 100 K Components3C-like proteinase Details Keywords HYDROLASE / SARS-CoV-2 / Coronavirus / main protease / 3CLpro / Mpro / ensemble refinement / temperature series / temperature / multitemperatureFunction / homology Function and homology informationFunction Domain/homology Component
Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / endopeptidase complex / 5'-3' RNA helicase activity / mRNA cap methyltransferase complex ... Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / endopeptidase complex / 5'-3' RNA helicase activity / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / positive regulation of RNA biosynthetic process / Lyases; Phosphorus-oxygen lyases / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific peptidase activity / SARS coronavirus main proteinase / suppression by virus of host type I interferon production / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / protein K48-linked deubiquitination / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / 7-methylguanosine mRNA capping / transcription, RNA-templated / viral transcription / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell Golgi apparatus / suppression by virus of host toll-like receptor signaling pathway / host cell endoplasmic reticulum / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive regulation of viral genome replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / positive stranded viral RNA replication / suppression by virus of host TRAF activity / protein autoprocessing / cysteine-type peptidase activity / helicase activity / ubiquitinyl hydrolase 1 / DNA helicase / DNA helicase activity / cysteine-type deubiquitinase activity / single-stranded RNA binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein processing / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / lyase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / suppression by virus of host gene expression / endonuclease activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / suppression by virus of host type I interferon-mediated signaling pathway / host cell cytoplasm / protein dimerization activity / host cell nucleus / ATP hydrolysis activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol Similarity search - Function RNA-dependent RNA polymerase, SARS-CoV-like / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. ... RNA-dependent RNA polymerase, SARS-CoV-like / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus proofreading exoribonuclease / Non-structural protein NSP16, coronavirus-like / Coronavirus RNA-dependent RNA polymerase, N-terminal / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Non-structural protein 14, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerisation / Nonstructural protein 15, middle domain, coronavirus / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Coronaviridae zinc-binding (CV ZBD) domain profile. / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Lipocalin signature. / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3c-M domain profile. / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Non-structural protein NSP1, betacoronavirus / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Non-structural protein NSP7, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP7 / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP8 / Coronavirus endopeptidase C30 / Coronavirus main protease (M-pro) domain profile. / Non-structural protein NSP7 superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein NSP8, coronavirus / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP6 / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Coronavirus papain-like peptidase / RNA synthesis protein NSP10, coronavirus Similarity search - Domain/homologyBiological species Severe acute respiratory syndrome coronavirus 2Method X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution : 1.55 Å DetailsAuthors Ebrahim, A. / Riley, B.T. / Kumaran, D. / Andi, B. / Fuchs, M.R. / McSweeney, S. / Keedy, D.A. Funding support United States, 7items Details Hide detailsOrganization Grant number Country National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM133769 United States Department of Energy (DOE, United States) National Virtual Biotechnology Laboratory (NVBL) United States Department of Energy (DOE, United States) Coronavirus CARES Act United States Department of Energy (DOE, United States) BNL LDRD 20-042 United States Department of Energy (DOE, United States) DE-SC0012704 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) P30GM133893 United States Department of Energy (DOE, United States) KP1605010 United States
CitationJournal : Biorxiv / Year : 2021Title : The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro ).Authors : Ebrahim, A. / Riley, B.T. / Kumaran, D. / Andi, B. / Fuchs, M.R. / McSweeney, S. / Keedy, D.A. History Deposition Apr 15, 2021 Deposition site : RCSB / Processing site : RCSBRevision 1.0 May 12, 2021 Provider : repository / Type : Initial releaseRevision 1.1 May 26, 2021 Group : Database references / Category : citation / citation_authorItem : _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCIDRevision 2.0 Apr 6, 2022 Group : Advisory / Atomic model ... Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary Category : atom_site / atom_site_anisotrop ... atom_site / atom_site_anisotrop / atom_type / chem_comp / citation_author / database_2 / database_PDB_caveat / entity / entity_src_gen / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_ls_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_keywords / struct_sheet_range / struct_site / struct_site_gen Item : _citation_author.identifier_ORCID / _database_2.pdbx_DOI ... _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_caveat.text / _entity_src_gen.gene_src_common_name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _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_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_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_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _software.version / _struct.title / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_keywords.text / _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 Description : Ligand identityDetails : X-ray fluorescence is consistent with the presence of Zn.Provider : author / Type : Coordinate replacement
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