2Z0S

Crystal structure of putative exosome complex RNA-binding protein

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)
A	d2z0sa1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	S1-domain of exosome complex RNA-binding protein 1, ECR1	(Aeropyrum pernix ) [TaxId: 56636 ],	SCOPe (2.08)
A	d2z0sa2	Alpha and beta proteins (a+b)	Eukaryotic type KH-domain (KH-domain type I)	Eukaryotic type KH-domain (KH-domain type I)	Eukaryotic type KH-domain (KH-domain type I)	Exosome complex RNA-binding protein 1, ECR1	(Aeropyrum pernix ) [TaxId: 56636 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Cold shock DNA-binding domain-like	8025651	4001909	SCOP2 (2022-06-29)
A	SCOP2 Family	Eukaryotic type KH-domain (KH-domain type I)	8025654	4001190	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8038030	3000135	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8038033	3001023	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)
A	S1_5	e2z0sA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_5	ECOD (1.6)
A	KH_6_2	e2z0sA3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Eukaryotic type KH-domain (KH-domain type I)	F: KH_6_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21266	RRP4, S1 domain (RRP4_S1)	RRP4, S1 domain	Exosome complex component RRP4 is a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. It consists of a N-terminal beta-sandw ...	Exosome complex component RRP4 is a non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. It consists of a N-terminal beta-sandwich hybrid domain (Pfam:PF14382), a central S1 domain and a C-terminal KH domain (Pfam:PF15985). This entry represents the S1 RNA binding domain, which has an OB fold [1,2].	Domain
A	PF00013	KH domain (KH_1)	KH domain	KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Probable exosome complex RNA-binding protein 1	RNA binding binding organic cyclic compound binding poly(A) binding poly-purine tract binding nucleic acid binding single-stranded RNA binding	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process RNA catabolic process	intracellular organelle intracellular anatomical structure organelle cellular anatomical entity exosome (RNase complex) protein-containing complex catalytic complex exoribonuclease complex cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR003029	S1 domain	Domain
A	IPR023474	Exosome complex component Rrp4	Family
A	IPR004087	K Homology domain	Domain
A	IPR048565	RRP4, S1 domain	Domain
A	IPR036612	K Homology domain, type 1 superfamily	Homologous Superfamily
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR026699	Exosome complex RNA-binding protein 1/RRP40/RRP4	Family
A	IPR004088	K Homology domain, type 1	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.