7AM1 | pdb_00007am1

Structure of yeast Ssd1, a pseudonuclease

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		e7am1A02	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F:	ECOD (v294.1)
A	Helicase_C	e7am1A04	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F: Helicase_C	ECOD (v294.1)

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
A, B	Protein SSD1	RNA binding binding nucleic acid binding mRNA binding mRNA 3'-UTR binding mRNA 5'-UTR binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity RNA binding binding nucleic acid binding mRNA binding mRNA 3'-UTR binding mRNA 5'-UTR binding 3'-5'-RNA exonuclease activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity, producing 5'-phosphomonoesters 3'-5' exonuclease activity RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exonuclease activity catalytic activity translation regulator activity mRNA regulatory element binding translation repressor activity translation repressor activity	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process localization macromolecule localization intracellular mRNA localization RNA localization catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process RNA catabolic process mRNA catabolic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleic acid catabolic process cell division regulation of cell cycle process cell cycle regulation of cell cycle regulation of G1 to G0 transition G1 to G0 transition cell cycle process regulation of fungal-type cell wall organization fungal-type cell wall organization regulation of cellular component organization regulation of cell wall organization or biogenesis cell wall organization or biogenesis cell wall organization cellular component organization fungal-type cell wall organization or biogenesis cellular component organization or biogenesis external encapsulating structure organization	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cellular bud P-body cellular bud neck intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule cellular bud P-body cellular bud neck site of polarized growth membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

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