4PMW | pdb_00004pmw

Structure of mouse Dis3L2 in complex with oligoU RNA substrate

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	KOG2102_1	e4pmwB2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG2102_1	ECOD (1.6)
B	Rrp44_CSD1	e4pmwB4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rrp44_CSD1	ECOD (1.6)
B	Rrp44_S1_like	e4pmwB3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rrp44_S1_like	ECOD (1.6)
B	RNB	e4pmwB1	A: beta barrels	X: OB-fold	H: RNB domain-like (From Topology)	T: RNB domain-like	F: RNB	ECOD (1.6)
A	KOG2102_1	e4pmwA3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG2102_1	ECOD (1.6)
A	Rrp44_CSD1	e4pmwA2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rrp44_CSD1	ECOD (1.6)
A	Rrp44_S1_like	e4pmwA4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rrp44_S1_like	ECOD (1.6)
A	RNB	e4pmwA1	A: beta barrels	X: OB-fold	H: RNB domain-like (From Topology)	T: RNB domain-like	F: RNB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.40.50.700	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	2.40.50.700	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF17849	Dis3-like cold-shock domain 2 (CSD2) (OB_Dis3)	Dis3-like cold-shock domain 2 (CSD2)	This domain has an OB fold and is found in the Dis3l2 protein [1]. This domain along with CSD1 binds to RNA.	Domain
A, B	PF00773	RNB domain (RNB)	RNB domain	This domain is the catalytic domain of ribonuclease II [1].	Domain
A, B	PF17877	DIS3-like exonuclease 2 C terminal (Dis3l2_C_term)	DIS3-like exonuclease 2 C terminal	This is the C-terminal S1 domain found in Dis3L2 proteins. Dis3L2 belongs to the RNase II/R 3-5 exonuclease superfamily, which includes the catalytic subunit of the RNA exosome in yeast and in humans [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	U-U-U-U-U-U-U-U-U-U-U-U-U-U	-	-	-
A, B	DIS3-like exonuclease 2	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity 3'-5'-RNA exonuclease activity RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding nuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity 3'-5'-RNA exonuclease activity RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity hydrolase activity hydrolase activity, acting on ester bonds exonuclease activity poly-pyrimidine tract binding RNA binding poly(U) RNA binding nucleic acid binding single-stranded RNA binding	cellular process cell cycle mitotic cell cycle regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process cellular process cell cycle mitotic cell cycle regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process mitotic nuclear division organelle fission chromosome organization sister chromatid segregation cellular component organization organelle organization nuclear division mitotic cell cycle process chromosome separation mitotic sister chromatid segregation nuclear chromosome segregation mitotic sister chromatid separation cellular component organization or biogenesis chromosome segregation cell cycle process developmental process multicellular organismal process maintenance of cell number stem cell population maintenance negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of mRNA metabolic process positive regulation of RNA metabolic process polyuridylation-dependent mRNA catabolic process positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process modification-dependent macromolecule catabolic process positive regulation of cellular process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process cell division miRNA catabolic process miRNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle organelle membraneless organelle supramolecular complex P-body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR028591	DIS3-like exonuclease 2	Family
A, B	IPR050180	RNR Ribonuclease	Family
A, B	IPR041505	Dis3-like cold-shock domain 2	Domain
A, B	IPR022966	Ribonuclease II/R, conserved site	Conserved Site
A, B	IPR033771	Rrp44-like cold shock domain	Domain
A, B	IPR001900	Ribonuclease II/R	Domain
A, B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, B	IPR041093	DIS3-like exonuclease 2-like, C-terminal	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.