Annotations: 5Z9X

Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with an RNA substrate

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e5z9xA1	A: alpha arrays	X: N-terminal domain of Small RNA Degrading Nuclease (SDN)	H: N-terminal domain of Small RNA Degrading Nuclease (SDN)	T: N-terminal domain of Small RNA Degrading Nuclease (SDN)	F:	ECOD (v295.2)
A		e5z9xA2	A: alpha arrays	X: P-loop domains-like	H: beta-propeller	T: 7-bladed	F:	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00929	Exonuclease (RNase_T)	Exonuclease	This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.;	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth R]	RNA (5'-R(PGPCPCPCPAPUPUPAP*G)-3')	-	-	-
A	Small RNA degrading nuclease 1	hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity regulatory RNA binding RNA binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters RNA exonuclease activity RNA nuclease activity regulatory RNA binding RNA binding binding miRNA binding nucleic acid binding	regulation of cellular process negative regulation of biological process pre-miRNA processing RNA metabolic process pre-miRNA 3'-end processing RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA 3'-end processing RNA processing regulatory ncRNA 3'-end processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of cellular process negative regulation of biological process pre-miRNA processing RNA metabolic process pre-miRNA 3'-end processing RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative regulation of cellular process RNA 3'-end processing RNA processing regulatory ncRNA 3'-end processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process miRNA processing regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process catabolic process miRNA catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process miRNA metabolic process RNA catabolic process ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis rRNA 3'-end processing cellular component organization or biogenesis rRNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR047021	RNA exonuclease REXO1/REXO3/REXO4-like	Family
A	IPR034922	RNA exonuclease 1-like, exonuclease domain	Domain
A	IPR013520	Ribonuclease H-like domain	Domain
A	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

5Z9X | pdb_00005z9x

Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with an RNA substrate

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage