8PX5 | pdb_00008px5

Structure of the RNA recognition motif (RRM) of Seb1 from S. pombe., solved at wavelength 2.75 A

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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	Rpb7-binding protein seb1	basal transcription machinery binding RNA polymerase binding protein binding binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase II C-terminal domain binding RNA polymerase core enzyme binding enzyme binding RNA binding snoRNA binding nucleic acid binding lncRNA binding chromatin-protein adaptor activity basal transcription machinery binding RNA polymerase binding protein binding binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase II C-terminal domain binding RNA polymerase core enzyme binding enzyme binding RNA binding snoRNA binding nucleic acid binding lncRNA binding chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process DNA-templated transcription termination DNA-templated transcription transcription by RNA polymerase II termination of RNA polymerase II transcription co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway 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 process regulatory ncRNA 3'-end processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process regulatory ncRNA processing regulatory ncRNA-mediated gene silencing 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 cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression pericentric heterochromatin formation constitutive heterochromatin formation negative regulation of gene expression, epigenetic	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle Mei2 nuclear dot complex intracellular organelle cellular anatomical structure organelle ribonucleoprotein complex

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 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.