6Y2E

Crystal structure of the free enzyme of the SARS-CoV-2 (2019-nCoV) main protease


ChainDomainClassArchitectureTopologyHomology
A2.40.10.10 Mainly Beta Beta Barrel Thrombin, subunit H Trypsin-like serine proteases
A2.40.10.10 Mainly Beta Beta Barrel Thrombin, subunit H Trypsin-like serine proteases
A2.40.10.10 Mainly Beta Beta Barrel Thrombin, subunit H Trypsin-like serine proteases
A1.10.1840.10 Mainly Alpha Orthogonal Bundle main proteinase (3clpro) structure, domain 3 main proteinase (3clpro) structure, domain 3

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
APF05409Coronavirus endopeptidase C30 (Peptidase_C30)Coronavirus endopeptidase C30- Family
APF19213Coronavirus replicase NSP6 (CoV_NSP6)Coronavirus replicase NSP6- Family
APF19211Coronavirus replicase NSP2, N-terminal (CoV_NSP2_N)Coronavirus replicase NSP2, N-terminal- Family
APF19212Coronavirus replicase NSP2, C-terminal (CoV_NSP2_C)Coronavirus replicase NSP2, C-terminal- Family
APF19217Coronavirus replicase NSP4, N-terminal (CoV_NSP4_N)Coronavirus replicase NSP4, N-terminal- Family
APF19218Coronavirus replicase NSP3, C-terminal (CoV_NSP3_C)Coronavirus replicase NSP3, C-terminal- Family
APF19215Coronavirus replicase NSP15, uridylate-specific endoribonuclease (CoV_NSP15_C)Coronavirus replicase NSP15, uridylate-specific endoribonucleaseThis entry represents the C-terminal domain of coronavirus non-structural protein 15 (NSP15 or nsp15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain exhibits endoribonuclease activity designated ...This entry represents the C-terminal domain of coronavirus non-structural protein 15 (NSP15 or nsp15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain exhibits endoribonuclease activity designated EndoU, highly conserved in all known CoVs and is part of the replicase-transcriptase complex that plays important roles in virus replication and transcription [1, 2, 3]. NSP15 is a Uridylate-specific endoribonuclease that cleaves the 5'-polyuridines from negative-sense viral RNA, termed PUN RNA either upstream or downstream of uridylates, at GUU or GU to produce molecules with 2',3'-cyclic phosphate ends [2, 3]. PUN RNA is a CoV MDA5-dependent pathogen-associated molecular pattern (PAMP) [3].
Domain
APF19216Coronavirus replicase NSP15, middle domain (CoV_NSP15_M)Coronavirus replicase NSP15, middle domainThis entry represents the non-catalytic middle domain from coronavirus non-structural protein 15 (NSP15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain is formed by ten beta strands organised in ...This entry represents the non-catalytic middle domain from coronavirus non-structural protein 15 (NSP15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain is formed by ten beta strands organised into three beta hairpins [1, 2].
Domain
APF16348Coronavirus replicase NSP4, C-terminal (CoV_NSP4_C)Coronavirus replicase NSP4, C-terminalThis is the C-terminal domain of the coronavirus nonstructural protein 4 (NSP4). NSP4 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. It is a membrane-spanning protein which is thought to anchor the viral replicati ...This is the C-terminal domain of the coronavirus nonstructural protein 4 (NSP4). NSP4 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. It is a membrane-spanning protein which is thought to anchor the viral replication-transcription complex (RTC) to modified endoplasmic reticulum membranes. This predominantly alpha-helical domain may be involved in protein-protein interactions [1]. It has been shown that in Betacoronavirus, the coexpression of NSP3 and NSP4 results in a membrane rearrangement to induce double-membrane vesicles (DMVs) and convoluted membranes (CMs), playing a critical role in SARS-CoV replication. There are two well conserved amino acid residues (H120 and F121) in NSP4 among Betacoronavirus, essential for membrane rearrangements during interaction with NSP3 [2,3].
Domain
APF19219Coronavirus replicase NSP15, N-terminal oligomerisation (CoV_NSP15_N)Coronavirus replicase NSP15, N-terminal oligomerisationThis is the N-terminal domain of the coronavirus nonstructural protein 15 (NSP15), which is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. NSP15, is a nidoviral RNA uridylate-specific endoribonuclease (NendoU) carryi ...This is the N-terminal domain of the coronavirus nonstructural protein 15 (NSP15), which is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. NSP15, is a nidoviral RNA uridylate-specific endoribonuclease (NendoU) carrying C-terminal catalytic domain belonging to the EndoU family. The SARS-CoV-2 NendoU monomers assemble into a double-ring hexamer, generated by a dimer of trimers. The hexamer is stabilized by the interactions of N-terminal oligomerization domain.
Domain
APF11501Betacoronavirus replicase NSP1 (bCoV_NSP1)Betacoronavirus replicase NSP1- Family
APF06460Coronavirus 2'-O-methyltransferase (CoV_Methyltr_2)Coronavirus 2'-O-methyltransferaseThis domain covers the NSP16 region of the coronavirus polyprotein. The SARS-CoV RNA cap SAM-dependent (nucleoside-2'-O-)-methyltransferase (2'-O-MTase) is a heterodimer comprising SARS-CoV nsp10 and nsp16. When bound to nsp10, nsp16 is active as a t ...This domain covers the NSP16 region of the coronavirus polyprotein. The SARS-CoV RNA cap SAM-dependent (nucleoside-2'-O-)-methyltransferase (2'-O-MTase) is a heterodimer comprising SARS-CoV nsp10 and nsp16. When bound to nsp10, nsp16 is active as a type-0 RNA cap-dependent 2'-O-MTase, ie., active only when the cap guanine is methylated at its N7 position. Nsp10 binds to nsp16 through an activation surface area in nsp10, and the resulting complex exhibits RNA cap (nucleoside-2'-O)-methyltransferase activity. Nsp10 is a double zinc finger protein together with nsp4, nsp5, nsp12, nsp14, and nsp16, nsp10 has been found to be essential in the assembly of a functional replication/transcription complex. Nsp16 adopts a typical fold of the S-adenosylmethionine-dependent methyltransferase (SAM) family as defined initially for the catechol O-MTase but it lacks several elements of the canonical MTase fold, such as helices B and C. The nsp16 topology matches those of dengue virus NS5 N-terminal domain and of vaccinia virus VP39 MTases [1, 2, 3].
Domain
APF12124Betacoronavirus SUD-C domain (bCoV_SUD_C)Betacoronavirus SUD-C domainThis domain is found in betacoronavirus non-structural protein NSP3, and is about 65 amino acids in length. It was originally thought to exist only in SARS-coronaviruses, and so was termed the SARS-unique domain (SUD), however this has since been ...This domain is found in betacoronavirus non-structural protein NSP3, and is about 65 amino acids in length. It was originally thought to exist only in SARS-coronaviruses, and so was termed the SARS-unique domain (SUD), however this has since been shown to be incorrect. The domain is also known as DPUP (domain preceding Ubl2 and PL2pro). NSP3 is the product of ORF1a, proteolytically released from the pp1a/1ab polyprotein [1,2]. The SUD domain has three globular domains, SUD-N (N-terminal), SUD-M (middle region of SUD), and SUD-C (C-terminal). SUD-C adopts a fold consisting of seven beta-strands arranged in an anti-parallel beta-sheet, and two alpha-helices which are packed against the same side of the beta-sheet. It adopts a frataxin like fold with structural similarities to DNA-binding domains. It has been shown that SUD-C binds to single-stranded RNA and recognises purine bases more strongly than pyrimidine bases, but these interactions are stabilised in the presence of SUD-M. The function of this domain is not clear but studies of structural homologues of SUD-C suggest that it could be related to metal, adenylate and nucleic acid binding [3].
Domain
APF00680Viral RNA-dependent RNA polymerase (RdRP_1)Viral RNA-dependent RNA polymerase- Family
APF16251Betacoronavirus nucleic acid-binding (NAR) (bCoV_NAR)Betacoronavirus nucleic acid-binding (NAR)This domain, approximately 100 residues in length, is found in the multidomain nonstructural protein NSP3, and described as NSP3e domain. NSP3 is part of Orf1a polyproteins in SARS-CoV [1]. It is an essential component of the replication/transcriptio ...This domain, approximately 100 residues in length, is found in the multidomain nonstructural protein NSP3, and described as NSP3e domain. NSP3 is part of Orf1a polyproteins in SARS-CoV [1]. It is an essential component of the replication/transcription complex [2]. The global domain of the NAR represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands and a group of residues form a positively charged patch on the protein surface as the binding site responsible for binding affinity for nucleic acids. When binding to ssRNA, the NAR prefers sequences with repeats of three consecutive Gs, such as (GGGA)5 and (GGGA)2. A positively charged surface patch (Lys75, Lys76, Lys99, and Arg106) is involved in RNA binding [2, 3].
Domain
APF11633Betacoronavirus single-stranded poly(A) binding domain (bCoV_SUD_M)Betacoronavirus single-stranded poly(A) binding domainThis domain identifies non-structural protein NSP3, the product of ORF1a in group 2 coronavirus. It is found in human SARS coronavirus polyprotein 1a and 1ab, and in related coronavirus polyproteins [1]. NSP3 binds to viral RNA, nucleocapsid protein, ...This domain identifies non-structural protein NSP3, the product of ORF1a in group 2 coronavirus. It is found in human SARS coronavirus polyprotein 1a and 1ab, and in related coronavirus polyproteins [1]. NSP3 binds to viral RNA, nucleocapsid protein, as well as other viral proteins, and participates in polyprotein processing [2]. The domain exhibits a macrodomain fold containing the nsp3 residues 528 to 648, with a flexibly extended N-terminal tail from residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. SUD-M(527-651) binds single-stranded poly(A); the contact area with this RNA on the protein surface, and the electrophoretic mobility shift assays confirm that SUD-M has higher affinity for purine bases than for pyrimidine bases [3].
Domain
APF12379Betacoronavirus replicase NSP3, N-terminal (bCoV_NSP3_N)Betacoronavirus replicase NSP3, N-terminal- Family
APF06471Coronavirus guanine-N7 methyltransferase (CoV_Methyltr_1)Coronavirus guanine-N7 methyltransferase- Family
APF09401Coronavirus RNA synthesis protein NSP10 (CoV_NSP10)Coronavirus RNA synthesis protein NSP10- Family
APF08715Coronavirus papain-like peptidase (CoV_peptidase)Coronavirus papain-like peptidase- Family
APF08716Coronavirus replicase NSP7 (CoV_NSP7)Coronavirus replicase NSP7NSP7 (non structural protein 7) has been implicated in viral RNA replication and is predominantly alpha helical in structure [1]. It forms a hexadecameric supercomplex with NSP8 that adopts a hollow cylinder-like structure [2]. The dimensions of the ...NSP7 (non structural protein 7) has been implicated in viral RNA replication and is predominantly alpha helical in structure [1]. It forms a hexadecameric supercomplex with NSP8 that adopts a hollow cylinder-like structure [2]. The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase [2]. NSP7 and NSP8 heterodimers play a role in the stabilisation of NSP12 regions involved in RNA binding and are essential for a highly active NSP12 polymerase complex [3].
Domain
APF06478Coronavirus RNA-dependent RNA polymerase, N-terminal (CoV_RPol_N)Coronavirus RNA-dependent RNA polymerase, N-terminal- Family
APF08717Coronavirus replicase NSP8 (CoV_NSP8)Coronavirus replicase NSP8Viral NSP8 (non structural protein 8) forms a hexadecameric supercomplex with NSP7 that adopts a hollow cylinder-like structure [1]. The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers pro ...Viral NSP8 (non structural protein 8) forms a hexadecameric supercomplex with NSP7 that adopts a hollow cylinder-like structure [1]. The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase [1]. NSP7 and NSP8 heterodimers play a role in the stabilisation of NSP12 regions involved in RNA binding and are essential for a highly active NSP12 polymerase complex [2]. It has been demonstrated that NSP8 acts as an oligo(U)-templated polyadenylyltransferase but also has robust (mono/oligo) adenylate transferase activities [3]. NSP8 has N- and C-terminal D/ExD/E conserved motifs, being the N-terminal motif critical for RNA polymerase activity as these residues are part of the Mg2-binding active site [4].
Domain
APF01661Macro domain (Macro)Macro domainThe Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently ...The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently [2]; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein [3]. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes.\t The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein [4]. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site [5].
Domain
APF08710Coronavirus replicase NSP9 (CoV_NSP9)Coronavirus replicase NSP9Nsp9 is a single-stranded RNA-binding viral protein involved in RNA synthesis [1]. Several crystallographic structures of nsp9 have shown that it is composed of seven beta strands and a single alpha helix. Nsp9 proteins have N-finger motifs and high ...Nsp9 is a single-stranded RNA-binding viral protein involved in RNA synthesis [1]. Several crystallographic structures of nsp9 have shown that it is composed of seven beta strands and a single alpha helix. Nsp9 proteins have N-finger motifs and highly conserved GXXXG motifs that both play critical roles in dimerisation [2]. The conserved helix-helix dimer interface containing a GXXXG protein-protein interaction motif is biologically relevant to SARS-CoV replication.
Domain
APF01443Viral (Superfamily 1) RNA helicase (Viral_helicase1)Viral (Superfamily 1) RNA helicase- Family

Gene Product Annotation Gene Product Annotation