2MOW | pdb_00002mow

Structure of Nrd1p CID - Trf4p NIM complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Pcf11 CTD-interacting domain (CID)-like	8046496	4002665	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ENTH/VHS domain-like	8053993	3000164	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	CTD_bind	e2mowA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: CTD_bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04818	CID domain (CID)	CID domain	-	Repeat

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 nucleic acid binding mRNA binding transcription regulatory region nucleic acid binding transcription regulatory region RNA binding regulatory region RNA binding	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 catabolic process macromolecule catabolic process nucleobase-containing compound catabolic process CUT catabolic process nucleic acid catabolic process RNA catabolic process snRNA 3'-end processing snRNA metabolic process snRNA processing nuclear RNA surveillance antisense RNA transcript catabolic process antisense RNA metabolic process RNA surveillance 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 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 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 termination of RNA polymerase II transcription, exosome-dependent DNA-templated transcription termination DNA-templated transcription transcription by RNA polymerase II 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 cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
B	Poly(A) RNA polymerase protein 2	catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding RNA binding nucleic acid binding mRNA binding poly(A) RNA polymerase activity adenylyltransferase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cation binding metal ion binding	nuclear RNA surveillance 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 sno(s)RNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process sno(s)RNA catabolic process nuclear RNA surveillance 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 sno(s)RNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process sno(s)RNA catabolic process RNA surveillance RNA catabolic process nuclear polyadenylation-dependent snoRNA catabolic process regulation of cellular process negative regulation of biological process regulation of primary metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality mRNA catabolic process regulation of biological process negative regulation of metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process polyadenylation-dependent mRNA catabolic process positive regulation of biological process mRNA destabilization regulation of mRNA catabolic process negative regulation of cellular process positive regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process RNA destabilization biological regulation regulation of macromolecule metabolic process regulation of catabolic process gene expression macromolecule biosynthetic process mRNA metabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process cell division nuclear polyadenylation-dependent antisense transcript catabolic process antisense RNA transcript catabolic process antisense RNA metabolic process nuclear polyadenylation-dependent CUT catabolic process CUT catabolic process snRNA metabolic process snRNA catabolic process nuclear polyadenylation-dependent snRNA catabolic process regulation of DNA recombination negative regulation of nucleobase-containing compound metabolic process DNA recombination DNA metabolic process negative regulation of DNA recombination negative regulation of DNA metabolic process regulation of DNA metabolic process U4 snRNA 3'-end processing nucleobase-containing compound biosynthetic process snRNA 3'-end processing RNA biosynthetic process nucleic acid biosynthetic process snRNA processing RNA 3'-end processing RNA processing histone mRNA catabolic process nuclear-transcribed mRNA catabolic process histone mRNA metabolic process tRNA modification tRNA metabolic process RNA modification tRNA processing macromolecule modification sexual reproduction reproductive process meiotic cell cycle meiotic cell cycle process meiotic DNA double-strand break formation meiosis I cell cycle process cell cycle cell cycle process nuclear mRNA surveillance of mRNA 3'-end processing nuclear mRNA surveillance modification-dependent macromolecule catabolic process polyadenylation-dependent RNA catabolic process polyadenylation-dependent ncRNA catabolic process RNA fragment catabolic process nuclear polyadenylation-dependent rRNA catabolic process cellular response to stimulus response to stimulus base-excision repair cellular response to stress DNA damage response response to stress DNA repair sno(s)RNA processing sno(s)RNA 3'-end processing poly(A)-dependent snoRNA 3'-end processing nuclear polyadenylation-dependent mRNA catabolic process TRAMP-dependent tRNA surveillance pathway tRNA surveillance tRNA decay	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol protein-containing complex TRAMP complex nuclear protein-containing 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
B	IPR054708	Poly(A) RNA polymerase, mitochondrial-like, central palm domain	Domain
B	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
B	IPR045862	Nucleotidyltransferase Trf4-like	Family
B	IPR002058	PAP/25A-associated	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.