5S6Z

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with PB2255187532

Present annotations:

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Product Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5s6za1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Nsp15 N-terminal domain-like	automated matches	2019-nCoV (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ]	SCOPe (2.08)
A	d5s6za2	Alpha and beta proteins (a+b)	EndoU-like	EndoU-like	Nsp15 C-terminal domain-like	automated matches	2019-nCoV (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ]	SCOPe (2.08)
A	d5s6za3	Artifacts	Tags	Tags	Tags	N-terminal Tags	2019-nCoV (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ]	SCOPe (2.08)
B	d5s6zb1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Nsp15 N-terminal domain-like	automated matches	2019-nCoV (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ]	SCOPe (2.08)
B	d5s6zb2	Alpha and beta proteins (a+b)	EndoU-like	EndoU-like	Nsp15 C-terminal domain-like	automated matches	2019-nCoV (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ]	SCOPe (2.08)
B	d5s6zb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	2019-nCoV (Severe acute respiratory syndrome coronavirus 2 ) [TaxId: 2697049 ]	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	EndoU-like	8092437	3000687	SCOP2B (2022-02-25)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8092436	3000118	SCOP2B (2022-02-25)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8092436	3000118	SCOP2B (2022-02-25)
B	SCOP2B Superfamily	EndoU-like	8092437	3000687	SCOP2B (2022-02-25)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	XendoU_like	e5s6zA2	A: a+b complex topology	X: RNase A-like	H: EndoU-like (From Topology)	T: EndoU-like	F: XendoU_like	ECOD (1.6)
A	NSP11_2nd	e5s6zA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: NSP11_2nd	ECOD (1.6)
B	XendoU_like	e5s6zB2	A: a+b complex topology	X: RNase A-like	H: EndoU-like (From Topology)	T: EndoU-like	F: XendoU_like	ECOD (1.6)
B	NSP11_2nd	e5s6zB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: NSP11_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Identifier	Description	Comments	Source
A, B	PF19215	Coronavirus replicase NSP15, uridylate-specific endoribonuclease (CoV_NSP15_C)	Coronavirus replicase NSP15, uridylate-specific endoribonuclease	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 ...	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
A, B	PF19216	Coronavirus replicase NSP15, middle domain (CoV_NSP15_M)	Coronavirus replicase NSP15, middle domain	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 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
A, B	PF19219	Coronavirus replicase NSP15, N-terminal oligomerisation (CoV_NSP15_N)	Coronavirus replicase NSP15, N-terminal oligomerisation	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) 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

Gene Product Annotation Gene Product Annotation

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Uridylate-specific endoribonuclease	catalytic activity endopeptidase activity cysteine-type endopeptidase activity peptidase activity cysteine-type peptidase activity hydrolase activity catalytic activity, acting on a protein DNA helicase activity helicase activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid ATP-dependent activity nuclease activity endonuclease activity hydrolase activity, acting on ester bonds exonuclease activity binding protein binding identical protein binding ubiquitin-like protein peptidase activity ISG15-specific peptidase activity methyltransferase activity transferase activity transferase activity, transferring one-carbon groups mRNA (nucleoside-2'-O-)-methyltransferase activity O-methyltransferase activity RNA methyltransferase activity mRNA methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity, acting on RNA protein dimerization activity protein homodimerization activity RNA helicase activity ATP-dependent activity, acting on RNA RNA-directed 5'-3' RNA polymerase activity transferase activity, transferring phosphorus-containing groups nucleotidyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity nucleic acid binding RNA binding single-stranded RNA binding organic cyclic compound binding heterocyclic compound binding cysteine-type deubiquitinase activity deubiquitinase activity zinc ion binding ion binding cation binding metal ion binding transition metal ion binding	metabolic process methylation viral process viral life cycle viral genome replication positive stranded viral RNA replication viral RNA genome replication response to external stimulus response to biotic stimulus cellular process modulation by virus of host process mitigation of host antiviral defense response modulation by virus of host cellular process mitigation of host defenses by symbiont modulation of process of another organism suppression by virus of host NF-kappaB cascade response to external biotic stimulus modulation by symbiont of host process modulation by symbiont of host cellular process biological process involved in symbiotic interaction biological process involved in interspecies interaction between organisms response to stimulus biological process involved in interaction with host response to other organism response to defenses of other organism response to host defenses response to host modulation by virus of host molecular function suppression by virus of host molecular function modulation by virus of host catalytic activity suppression by virus of host TRAF-mediated signal transduction suppression by virus of host TRAF activity modulation of signal transduction in another organism modulation by symbiont of host signal transduction pathway suppression by symbiont of host signal transduction pathway negative regulation by symbiont of host catalytic activity modulation by symbiont of host molecular function modulation by symbiont of host catalytic activity viral gene expression viral protein processing viral transcription	host cellular component host cell cytoplasm host cell part host intracellular part host cell cytoplasm part viral factory cytoplasmic viral factory host intracellular region host cell cellular anatomical entity host intracellular organelle host intracellular membrane-bounded organelle host cell endoplasmic reticulum-Golgi intermediate compartment host cell membrane host cell perinuclear region of cytoplasm membrane integral component of membrane intrinsic component of membrane

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.