5EU8

Structure of FIPV main protease in complex with dual inhibitors


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
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
APF13087AAA domain (AAA_12)AAA domainThis family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.Domain
APF16688Replicase polyprotein N-term from Coronavirus nsp1 (CNV-Replicase_N)Replicase polyprotein N-term from Coronavirus nsp1CNV-Replicase_N is the N-terminal domain of a family of ssRNA positive-stranded porcine transmissible gastroenteritis coronaviruses. the domain folds into a six-stranded beta-barrel fold with a long alpha helix on the rim of the barrel. This fold is ...CNV-Replicase_N is the N-terminal domain of a family of ssRNA positive-stranded porcine transmissible gastroenteritis coronaviruses. the domain folds into a six-stranded beta-barrel fold with a long alpha helix on the rim of the barrel. This fold is shared with SARS-CoV nsp1 [1].
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
APF06471Coronavirus guanine-N7 methyltransferase (CoV_Methyltr_1)Coronavirus guanine-N7 methyltransferase- 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
APF09401Coronavirus RNA synthesis protein NSP10 (CoV_NSP10)Coronavirus RNA synthesis protein NSP10- Family
APF08715Coronavirus papain-like peptidase (CoV_peptidase)Coronavirus papain-like peptidase- Family
APF06478Coronavirus RNA-dependent RNA polymerase, N-terminal (CoV_RPol_N)Coronavirus RNA-dependent RNA polymerase, N-terminal- 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
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
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
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

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Amain protease
BN-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDEnone none none