Annotations: 2VNU

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth D]	d2vnud2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exosome complex exonuclease RRP44, C-terminal domain	BAKERS YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B [auth D]	d2vnud1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exosome complex exonuclease RRP44, middle domain	BAKERS YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B [auth D]	d2vnud3	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Exosome complex exonuclease RRP44, N-terminal domain	BAKERS YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B [auth D]	d2vnud4	All beta proteins	OB-fold	Nucleic acid-binding proteins	RNB domain-like	Exosome complex exonuclease RRP44	BAKERS YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth D]	SCOP2 Family	Cold shock DNA-binding domain-like	8025235	4001909	SCOP2 (2022-06-29)
B [auth D]	SCOP2 Family	Cold shock DNA-binding domain-like	8025237	4001909	SCOP2 (2022-06-29)
B [auth D]	SCOP2 Family	Cold shock DNA-binding domain-like	8025238	4001909	SCOP2 (2022-06-29)
B [auth D]	SCOP2 Family	RNB domain-like	8025239	4001753	SCOP2 (2022-06-29)
B [auth D]	SCOP2 Superfamily	Nucleic acid-binding proteins	8037614	3000135	SCOP2 (2022-06-29)
B [auth D]	SCOP2 Superfamily	Nucleic acid-binding proteins	8037616	3000135	SCOP2 (2022-06-29)
B [auth D]	SCOP2 Superfamily	Nucleic acid-binding proteins	8037617	3000135	SCOP2 (2022-06-29)
B [auth D]	SCOP2 Superfamily	Nucleic acid-binding proteins	8037618	3000135	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth D]	Rrp44_S1	e2vnuD2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rrp44_S1	ECOD (1.6)
B [auth D]	KOG2102	e2vnuD1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: KOG2102	ECOD (1.6)
B [auth D]	Rrp44_CSD1	e2vnuD3	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 [auth D]	RNB	e2vnuD4	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 [auth D]	2.40.50.690	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B [auth D]	2.40.50.700	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B [auth D]	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
B [auth D]	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
B [auth D]	PF17215	S1 domain (Rrp44_S1)	S1 domain	This domain corresponds to the S1 domain found at the C-terminus of ribonucleases such as yeast Rrp44 [1].	Domain
B [auth D]	PF17216	Rrp44-like cold shock domain (Rrp44_CSD1)	Rrp44-like cold shock domain		Domain
B [auth D]	PF00773	RNB domain (RNB)	RNB domain	This domain is the catalytic domain of ribonuclease II [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	5'-R(APAPAPAPAPAPAPAPAPAP)-3'	-	-	-
B [auth D]	EXOSOME COMPLEX EXONUCLEASE RRP44	3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity RNA binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exonuclease activity catalytic activity RNA binding binding tRNA binding nucleic acid binding endonuclease activity RNA endonuclease activity	nonfunctional rRNA decay catabolic process RNA metabolic process primary metabolic process rRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process rRNA metabolic process nonfunctional rRNA decay catabolic process RNA metabolic process primary metabolic process rRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process rRNA metabolic process RNA catabolic process nuclear RNA surveillance nuclear polyadenylation-dependent CUT catabolic process CUT metabolic process CUT catabolic process RNA surveillance ribonucleoprotein complex biogenesis exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) rRNA processing cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process RNA 3'-end processing cellular component organization or biogenesis RNA processing maturation of 5.8S rRNA gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) biosynthetic process rRNA 3'-end processing regulation of cellular process negative regulation of biological process negative regulation of cellular 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 nuclear mRNA surveillance biological regulation regulation of macromolecule metabolic process mRNA metabolic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process mRNA processing nuclear mRNA surveillance of mRNA 3'-end processing nuclear polyadenylation-dependent rRNA catabolic process regulatory ncRNA 3'-end processing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing tRNA metabolic process TRAMP-dependent tRNA surveillance pathway tRNA surveillance tRNA decay	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen exosome (RNase complex) protein-containing complex catalytic complex exoribonuclease complex cytoplasmic exosome (RNase complex) nuclear protein-containing complex nuclear exosome (RNase complex)

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D]	IPR050180	RNR Ribonuclease	Family
B [auth D]	IPR041505	Dis3-like cold-shock domain 2	Domain
B [auth D]	IPR003029	S1 domain	Domain
B [auth D]	IPR022966	Ribonuclease II/R, conserved site	Conserved Site
B [auth D]	IPR033770	Exosome complex exonuclease RRP44, S1 domain	Domain
B [auth D]	IPR033771	Rrp44-like cold shock domain	Domain
B [auth D]	IPR002716	PIN domain	Domain
B [auth D]	IPR001900	Ribonuclease II/R	Domain
B [auth D]	IPR029060	PIN-like domain superfamily	Homologous Superfamily
B [auth D]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily

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.