1YZ9 | pdb_00001yz9

Crystal structure of RNase III mutant E110Q from Aquifex aeolicus complexed with double stranded RNA at 2.1-Angstrom Resolution

External Resource: Annotation

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth B]	d1yz9b1	All alpha proteins	RNase III domain-like	RNase III domain-like	RNase III catalytic domain-like	RNase III endonuclease catalytic domain	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
F [auth B]	d1yz9b2	Alpha and beta proteins (a+b)	dsRBD-like	dsRNA-binding domain-like	Double-stranded RNA-binding domain (dsRBD)	RNase III, C-terminal domain	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
E [auth A]	d1yz9a1	All alpha proteins	RNase III domain-like	RNase III domain-like	RNase III catalytic domain-like	RNase III endonuclease catalytic domain	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
E [auth A]	d1yz9a2	Alpha and beta proteins (a+b)	dsRBD-like	dsRNA-binding domain-like	Double-stranded RNA-binding domain (dsRBD)	RNase III, C-terminal domain	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth B]	SCOP2B Superfamily	dsRNA-binding domain-like	8034892	3000985	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	RNase III domain-like	8034890	3001839	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	RNase III domain-like	8034890	3001839	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	dsRNA-binding domain-like	8034892	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)
F [auth B]	Ribonucleas_3_3	e1yz9B1	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)
F [auth B]	dsrm	e1yz9B2	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)
E [auth A]	Ribonucleas_3_3	e1yz9A1	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)
E [auth A]	dsrm	e1yz9A2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth B]	1.10.1520.10	Mainly Alpha	Orthogonal Bundle	Ribonuclease iii, N-terminal Endonuclease Domain	Chain A	CATH (4.3.0)
F [auth B]	3.30.160.20	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain		CATH (4.3.0)
E [auth A]	1.10.1520.10	Mainly Alpha	Orthogonal Bundle	Ribonuclease iii, N-terminal Endonuclease Domain	Chain A	CATH (4.3.0)
E [auth A]	3.30.160.20	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B]	PF00636	Ribonuclease III domain (Ribonuclease_3)	Ribonuclease III domain	-	Family
E [auth A], F [auth B]	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
A [auth C], B [auth D], C [auth E], D [auth F]	5'-R(CPGPAPAPCPUPUPCPGPCP*G)-3'	-	-	-
E [auth A], F [auth B]	Ribonuclease III	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 cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding	regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing nucleobase-containing compound biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process tRNA metabolic process tRNA processing mRNA processing mRNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR011907	Ribonuclease III	Family
E [auth A], F [auth B]	IPR036389	Ribonuclease III, endonuclease domain superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR000999	Ribonuclease III domain	Domain
E [auth A], F [auth B]	IPR014720	Double-stranded RNA-binding 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.