Annotations: 5O1X

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RRM_1_3	e5o1xA1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: RRM_1_3	ECOD (1.6)
A	KOG0132	e5o1xA2	A: a+b two layers	X: Seb1 domain 2 (From Topology)	H: Seb1 domain 2 (From Topology)	T: Seb1 domain 2	F: KOG0132	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00076	RNA recognition motif (RRM_1)	RNA recognition motif	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and pro ...	The RRM motif (a.k.a. RRM, RBD, or RNP domain) is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins (Swiss:P05455) have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins (Swiss:P05455) are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.	Domain
A	PF21380	Nrd1/Seb1, domain 2 (Nrd1-Seb1_dom2)	Nrd1/Seb1, domain 2	Nrd1 is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein, part of the Nrd1-Nab3-Sen1 (NNS) complex which is involved in the termination and processing of short RNA polymerase II transcripts [1]. Seb1 is the Nrd1 homologue fr ...	Nrd1 is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein, part of the Nrd1-Nab3-Sen1 (NNS) complex which is involved in the termination and processing of short RNA polymerase II transcripts [1]. Seb1 is the Nrd1 homologue from S. pombe that is essential for cell viability and binds directly to Rpb7 subunit of RNA polymerase II. It functions in terminating all classes of Pol II-transcribed genes genome-wide. These proteins have a RNA-recognition motif (RRM, Pfam:PF00076) fused to a second alpha/beta domain described as domain 2 (also referred to as the split domain, SD, in [3]) from Nrd1 and Seb1. This domain is essential and forms a rigid body with the canonical RRM that interacts with RNA [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Protein NRD1	protein binding binding protein domain specific binding RNA binding organic cyclic compound binding nucleic acid binding mRNA binding transcription regulatory region nucleic acid binding transcription regulatory region RNA binding regulatory region RNA binding	cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process cellular biosynthetic process mRNA 3'-end processing cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process nucleic acid catabolic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process CUT metabolic process CUT catabolic process snRNA 3'-end processing snRNA metabolic process ncRNA metabolic process snRNA processing nuclear RNA surveillance catabolic process antisense RNA transcript catabolic process macromolecule catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process antisense RNA metabolic process RNA surveillance organic substance catabolic process RNA catabolic process sno(s)RNA processing sno(s)RNA 3'-end processing sno(s)RNA metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process nuclear-transcribed mRNA catabolic process nuclear mRNA surveillance biological regulation regulation of macromolecule metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process DNA-templated transcription termination RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II termination of RNA polymerase II transcription, exosome-dependent nucleobase-containing compound biosynthetic process organic cyclic compound biosynthetic process termination of RNA polymerase II transcription tRNA metabolic process tRNA processing tRNA 3'-end processing	protein-containing complex Nrd1 complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR048892	Nrd1/Seb1, domain 2	Domain
A	IPR034894	Nrd1/Seb1, RNA recognition motif	Domain
A	IPR008942	ENTH/VHS	Homologous Superfamily
A	IPR000504	RNA recognition motif domain	Domain
A	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A	IPR006569	CID domain	Domain
A	IPR035979	RNA-binding domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.