6O3X | pdb_00006o3x

Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM2

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	SCOP2B Superfamily	ENTH/VHS domain-like	8053993	3000164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ENTH/VHS domain-like	8053993	3000164	SCOP2B (2022-06-29)
A	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	Sigma70_r2,Sigma70_ner	e6o3xC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma70_r2,Sigma70_ner	ECOD (v294.1)
B	Sigma70_r2,Sigma70_ner	e6o3xB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sigma70_r2,Sigma70_ner	ECOD (v294.1)
A		e6o3xA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (utative)
B	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (utative)
A	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
A, B, C	PF04818	CID domain (CID)	CID domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E, F	Helicase SEN1	nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity protein binding binding protein domain specific binding nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity protein binding binding protein domain specific binding catalytic activity, acting on RNA ATP-dependent activity, acting on RNA DNA/RNA helicase activity hydrolase activity RNA binding nucleic acid binding 5'-3' DNA/RNA helicase activity 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 response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription termination nucleic acid metabolic process RNA biosynthetic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription termination nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process termination of RNA polymerase II transcription DNA-templated DNA replication DNA replication DNA-templated DNA replication maintenance of fidelity DNA metabolic process sno(s)RNA processing sno(s)RNA 3'-end processing sno(s)RNA metabolic 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 transcription-coupled nucleotide-excision repair nucleotide-excision repair DNA repair ribosomal small subunit biogenesis maturation of SSU-rRNA mRNA 3'-end processing mRNA processing mRNA metabolic process termination of RNA polymerase III transcription transcription by RNA polymerase III 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 macromolecule metabolic 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 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 replication fork chromosome protein-containing complex preribosome nuclear protein-containing complex small-subunit processome ribonucleoprotein complex nuclear body nucleoplasm Nrd1 complex
A, B, C	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, E, F	IPR041677	DNA2/NAM7 helicase, helicase domain	Domain
D, E, F	IPR045055	DNA2/NAM7-like helicase	Family
D, E, F	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
D, E, F	IPR024481	Helicase Sen1, N-terminal	Domain
D, E, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
D, E, F	IPR044340	Helicase Sen1, 1B domain	Domain
D, E, F	IPR047187	Upf1-like, C-terminal helicase domain	Domain
D, E, F	IPR056474	Helicase SEN1, beta-barrel domain	Domain
A, B, C	IPR048892	Nrd1/Seb1, domain 2	Domain
A, B, C	IPR034894	Nrd1/Seb1, RNA recognition motif	Domain
A, B, C	IPR008942	ENTH/VHS	Homologous Superfamily
A, B, C	IPR000504	RNA recognition motif domain	Domain
A, B, C	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, B, C	IPR006569	CID domain	Domain
A, B, C	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.