6O3W

Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM1

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)
C [auth A]	SCOP2B Superfamily	ENTH/VHS domain-like	8053993	3000164	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	ENTH/VHS domain-like	8053993	3000164	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth A]	PF04818	e6o3wA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF04818	ECOD (1.6)
D [auth B]	PF04818	e6o3wB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF04818	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (utative)
D [auth B]	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	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 [auth C], B [auth D]	Helicase SEN1	ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity protein binding binding protein domain specific binding hydrolase activity RNA binding organic cyclic compound binding ATP-dependent activity, acting on DNA DNA helicase activity catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity protein binding binding protein domain specific binding hydrolase activity RNA binding organic cyclic compound binding nucleic acid binding DNA/RNA helicase activity catalytic activity, acting on RNA 5'-3' DNA/RNA helicase activity ATP-dependent activity, acting on RNA 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 mRNA binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription termination site sequence-specific DNA binding transcription regulatory region nucleic acid binding	cellular biosynthetic process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression cellular biosynthetic process RNA metabolic process DNA-templated transcription termination RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process organic substance biosynthetic process cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process macromolecule metabolic process termination of RNA polymerase II transcription DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity DNA metabolic process DNA replication sno(s)RNA processing sno(s)RNA 3'-end processing sno(s)RNA metabolic process ncRNA metabolic process nucleic acid catabolic process RNA 3'-end processing RNA processing ribonucleoprotein complex biogenesis rRNA processing cellular component biogenesis ribosome biogenesis cellular component organization or biogenesis rRNA metabolic process tRNA metabolic process tRNA processing cellular response to stimulus response to stimulus transcription-coupled nucleotide-excision repair cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair maturation of SSU-rRNA ribosomal small subunit biogenesis mRNA 3'-end processing mRNA processing mRNA metabolic process cell redox homeostasis cellular homeostasis homeostatic process snRNA metabolic process snRNA processing regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process flocculation regulation of cell adhesion biological process involved in intraspecies interaction between organisms negative regulation of biological process negative regulation of cell adhesion negative regulation of flocculation cell adhesion cell-cell adhesion negative regulation of cell-cell adhesion negative regulation of cellular process regulation of cell-cell adhesion regulation of flocculation adhesion between unicellular organisms	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle cytoplasm replication fork chromosome preribosome protein-containing complex ribonucleoprotein complex small-subunit processome nuclear body nucleoplasm Nrd1 complex
C [auth A], D [auth B]	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 [auth C], B [auth D]	IPR041677	DNA2/NAM7 helicase, helicase domain	Domain
A [auth C], B [auth D]	IPR045055	DNA2/NAM7-like helicase	Family
A [auth C], B [auth D]	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
A [auth C], B [auth D]	IPR024481	Helicase Sen1, N-terminal	Domain
A [auth C], B [auth D]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth C], B [auth D]	IPR044340	Helicase Sen1, 1B domain	Domain
A [auth C], B [auth D]	IPR047187	Upf1-like, C-terminal helicase domain	Domain
C [auth A], D [auth B]	IPR048892	Nrd1/Seb1, domain 2	Domain
C [auth A], D [auth B]	IPR034894	Nrd1/Seb1, RNA recognition motif	Domain
C [auth A], D [auth B]	IPR008942	ENTH/VHS	Homologous Superfamily
C [auth A], D [auth B]	IPR000504	RNA recognition motif domain	Domain
C [auth A], D [auth B]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR006569	CID domain	Domain
C [auth A], D [auth B]	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 R01GM133198.