5T16 | pdb_00005t16

Crystal structure of yeast RNase III (Rnt1p) complexed with a non-hydrolyzable RNA substrate analog

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	dsRNA-binding domain-like	8039971	3000985	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	dsRNA-binding domain-like	8039971	3000985	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	dsRNA-binding domain-like	8039971	3000985	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	dsRNA-binding domain-like	8039971	3000985	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
N	KOG1817_2nd	e5t16N1	A: alpha arrays	X: Ribonuclease 3 N-terminal domain (From Topology)	H: Ribonuclease 3 N-terminal domain (From Topology)	T: Ribonuclease 3 N-terminal domain	F: KOG1817_2nd	ECOD (1.6)
M	KOG1817_2nd	e5t16M1	A: alpha arrays	X: Ribonuclease 3 N-terminal domain (From Topology)	H: Ribonuclease 3 N-terminal domain (From Topology)	T: Ribonuclease 3 N-terminal domain	F: KOG1817_2nd	ECOD (1.6)
L	KOG1817_2nd	e5t16L1	A: alpha arrays	X: Ribonuclease 3 N-terminal domain (From Topology)	H: Ribonuclease 3 N-terminal domain (From Topology)	T: Ribonuclease 3 N-terminal domain	F: KOG1817_2nd	ECOD (1.6)
K	KOG1817_2nd	e5t16K1	A: alpha arrays	X: Ribonuclease 3 N-terminal domain (From Topology)	H: Ribonuclease 3 N-terminal domain (From Topology)	T: Ribonuclease 3 N-terminal domain	F: KOG1817_2nd	ECOD (1.6)
F	KOG1817_2nd	e5t16F1	A: alpha arrays	X: Ribonuclease 3 N-terminal domain (From Topology)	H: Ribonuclease 3 N-terminal domain (From Topology)	T: Ribonuclease 3 N-terminal domain	F: KOG1817_2nd	ECOD (1.6)
E	KOG1817_2nd	e5t16E1	A: alpha arrays	X: Ribonuclease 3 N-terminal domain (From Topology)	H: Ribonuclease 3 N-terminal domain (From Topology)	T: Ribonuclease 3 N-terminal domain	F: KOG1817_2nd	ECOD (1.6)
D	KOG1817_2nd	e5t16D1	A: alpha arrays	X: Ribonuclease 3 N-terminal domain (From Topology)	H: Ribonuclease 3 N-terminal domain (From Topology)	T: Ribonuclease 3 N-terminal domain	F: KOG1817_2nd	ECOD (1.6)
C	KOG1817_2nd	e5t16C1	A: alpha arrays	X: Ribonuclease 3 N-terminal domain (From Topology)	H: Ribonuclease 3 N-terminal domain (From Topology)	T: Ribonuclease 3 N-terminal domain	F: KOG1817_2nd	ECOD (1.6)
J	Ribonucleas_3_3	e5t16J1	A: alpha arrays	X: RNase III catalytic domain-like (From Topology)	H: RNase III catalytic domain-like (From Topology)	T: RNase III catalytic domain-like	F: Ribonucleas_3_3	ECOD (1.6)
J	dsrm	e5t16J2	A: a+b two layers	X: dsRBD-like	H: dsRNA-binding domain-like (From Topology)	T: dsRNA-binding domain-like	F: dsrm	ECOD (1.6)
I	Ribonucleas_3_3	e5t16I1	A: alpha arrays	X: RNase III catalytic domain-like (From Topology)	H: RNase III catalytic domain-like (From Topology)	T: RNase III catalytic domain-like	F: Ribonucleas_3_3	ECOD (1.6)
I	dsrm	e5t16I2	A: a+b two layers	X: dsRBD-like	H: dsRNA-binding domain-like (From Topology)	T: dsRNA-binding domain-like	F: dsrm	ECOD (1.6)
B	Ribonucleas_3_3	e5t16B1	A: alpha arrays	X: RNase III catalytic domain-like (From Topology)	H: RNase III catalytic domain-like (From Topology)	T: RNase III catalytic domain-like	F: Ribonucleas_3_3	ECOD (1.6)
B	dsrm	e5t16B2	A: a+b two layers	X: dsRBD-like	H: dsRNA-binding domain-like (From Topology)	T: dsRNA-binding domain-like	F: dsrm	ECOD (1.6)
A	Ribonucleas_3_3	e5t16A2	A: alpha arrays	X: RNase III catalytic domain-like (From Topology)	H: RNase III catalytic domain-like (From Topology)	T: RNase III catalytic domain-like	F: Ribonucleas_3_3	ECOD (1.6)
A	dsrm	e5t16A1	A: a+b two layers	X: dsRBD-like	H: dsRNA-binding domain-like (From Topology)	T: dsRNA-binding domain-like	F: dsrm	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D, E, F, K C, D, E, F, K, L, M, N	PF18497	Ribonuclease III N-terminal domain (RNase_3_N)	Ribonuclease III N-terminal domain	This is the N-terminal domain of eukaryotic ribonuclease 3 (RNase III, EC:3.1.26.3). Structure analysis of Saccharomyces cerevisiaeRNase III (Rnt1p) :RNA revealed specific contacts between the N-terminal domain (NTD) dimer and the 5' end region of th ...	This is the N-terminal domain of eukaryotic ribonuclease 3 (RNase III, EC:3.1.26.3). Structure analysis of Saccharomyces cerevisiaeRNase III (Rnt1p) :RNA revealed specific contacts between the N-terminal domain (NTD) dimer and the 5' end region of the tetraloop. Deletion of the NTD led to cleavage at alternative site(s), suggesting that this region increases the precision of the cleavage site selectivity [1].	Domain
A, B, I, J	PF00636	Ribonuclease III domain (Ribonuclease_3)	Ribonuclease III domain	-	Family
A, B, I, J	PF00035	Double-stranded RNA binding motif (dsrm)	Double-stranded RNA binding motif	Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localisation of at least five d ...	Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localisation of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, O, P	RNA substrate analog	-	-	-
C, D, E, F, K C, D, E, F, K, L, M, N	Ribonuclease 3	RNA binding double-stranded RNA binding binding nucleic acid binding ribonuclease III activity double-stranded RNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA binding double-stranded RNA binding binding nucleic acid binding ribonuclease III activity double-stranded RNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity	sno(s)RNA processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process box C/D sno(s)RNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process box C/D sno(s)RNA processing nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process sno(s)RNA metabolic process sno(s)RNA processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process box C/D sno(s)RNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process box C/D sno(s)RNA processing nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process sno(s)RNA metabolic process metabolic process cellular process macromolecule metabolic process RNA processing DNA-templated transcription termination DNA-templated transcription transcription by RNA polymerase II termination of RNA polymerase II transcription box H/ACA sno(s)RNA processing box H/ACA sno(s)RNA metabolic process rRNA transcription rRNA metabolic process U5 snRNA 3'-end processing snRNA 3'-end processing snRNA metabolic process snRNA processing RNA 3'-end processing ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis U4 snRNA 3'-end processing termination of RNA polymerase II transcription, exosome-dependent U1 snRNA 3'-end processing regulation of fungal-type cell wall organization fungal-type cell wall organization regulation of biological process regulation of cellular process regulation of cellular component organization regulation of cell wall organization or biogenesis cell wall organization or biogenesis biological regulation cell wall organization cellular component organization fungal-type cell wall organization or biogenesis external encapsulating structure organization chromatin organization	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nucleoplasm
A, B, I, J	Ribonuclease 3	RNA binding double-stranded RNA binding binding nucleic acid binding ribonuclease III activity double-stranded RNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA binding double-stranded RNA binding binding nucleic acid binding ribonuclease III activity double-stranded RNA-specific ribonuclease activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity catalytic activity	sno(s)RNA processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process box C/D sno(s)RNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process box C/D sno(s)RNA processing nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process sno(s)RNA metabolic process sno(s)RNA processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process box C/D sno(s)RNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process box C/D sno(s)RNA processing nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process sno(s)RNA metabolic process metabolic process cellular process macromolecule metabolic process RNA processing DNA-templated transcription termination DNA-templated transcription transcription by RNA polymerase II termination of RNA polymerase II transcription box H/ACA sno(s)RNA processing box H/ACA sno(s)RNA metabolic process rRNA transcription rRNA metabolic process U5 snRNA 3'-end processing snRNA 3'-end processing snRNA metabolic process snRNA processing RNA 3'-end processing ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis U4 snRNA 3'-end processing termination of RNA polymerase II transcription, exosome-dependent U1 snRNA 3'-end processing regulation of fungal-type cell wall organization fungal-type cell wall organization regulation of biological process regulation of cellular process regulation of cellular component organization regulation of cell wall organization or biogenesis cell wall organization or biogenesis biological regulation cell wall organization cellular component organization fungal-type cell wall organization or biogenesis external encapsulating structure organization chromatin organization	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D, E, F, K C, D, E, F, K, L, M, N	IPR044449	Rnt1/Pac1, double-stranded RNA binding domain, fungi	Domain
C, D, E, F, K C, D, E, F, K, L, M, N	IPR036389	Ribonuclease III, endonuclease domain superfamily	Homologous Superfamily
C, D, E, F, K C, D, E, F, K, L, M, N	IPR000999	Ribonuclease III domain	Domain
C, D, E, F, K C, D, E, F, K, L, M, N	IPR014720	Double-stranded RNA-binding domain	Domain
C, D, E, F, K C, D, E, F, K, L, M, N	IPR040540	Ribonuclease III, N-terminal domain	Domain
A, B, I, J	IPR044449	Rnt1/Pac1, double-stranded RNA binding domain, fungi	Domain
A, B, I, J	IPR036389	Ribonuclease III, endonuclease domain superfamily	Homologous Superfamily
A, B, I, J	IPR000999	Ribonuclease III domain	Domain
A, B, I, J	IPR014720	Double-stranded RNA-binding domain	Domain
A, B, I, J	IPR040540	Ribonuclease III, N-terminal domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.