Annotations: 3NYB

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	zf-CCHC	e3nybB2	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: zf-CCHC	ECOD (1.6)
B	AIR1_2nd	e3nybB1	A: few secondary structure elements	X: CCHC-type 1 zinc finger	H: CCHC-type 1 zinc finger (From Topology)	T: CCHC-type 1 zinc finger	F: AIR1_2nd	ECOD (1.6)
A	PAP_assoc	e3nybA4	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: PAP/OAS1 substrate-binding domain	F: PAP_assoc	ECOD (1.6)
A	PAP_central_1st_1	e3nybA3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: PAP_central_1st_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	4.10.60.10	Few Secondary Structures	Irregular	HIV-1 Nucleocapsid Protein	Zinc finger, CCHC-type	CATH (4.3.0)
A	1.10.1410.10	Mainly Alpha	Orthogonal Bundle	Poly(a)-polymerase, middle domain		CATH (4.3.0)
A	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00098	Zinc knuckle (zf-CCHC)	Zinc knuckle	The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eu ...	The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.	Domain
B	PF21759	AIR2-like, CCHC-type 1 zinc finger 4 (AIR2-like_ZnK4)	AIR2-like, CCHC-type 1 zinc finger 4	-	Motif
A	PF03828	Cid1 family poly A polymerase (PAP_assoc)	Cid1 family poly A polymerase	-	Family
A	PF01909	Nucleotidyltransferase domain (NTP_transf_2)	Nucleotidyltransferase domain	Members of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTa ...	Members of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Protein AIR2	molecular adaptor activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding protein-macromolecule adaptor activity	catabolic process RNA metabolic process primary metabolic process macromolecule catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process modification-dependent macromolecule catabolic process polyadenylation-dependent RNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process catabolic process RNA metabolic process primary metabolic process macromolecule catabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process modification-dependent macromolecule catabolic process polyadenylation-dependent RNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process tRNA modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process tRNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification RNA processing regulation of cellular process negative regulation of biological process negative regulation of cellular process nuclear mRNA surveillance of mRNA 3'-end processing RNA surveillance negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear RNA surveillance nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process nuclear mRNA surveillance biological regulation regulation of macromolecule metabolic process mRNA 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 RNA fragment catabolic process sno(s)RNA metabolic process sno(s)RNA catabolic process nuclear polyadenylation-dependent snoRNA catabolic process nuclear polyadenylation-dependent rRNA catabolic process nuclear polyadenylation-dependent CUT catabolic process CUT catabolic process snRNA metabolic process snRNA catabolic process nuclear polyadenylation-dependent snRNA 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 protein-containing complex TRAMP complex nuclear protein-containing complex
A	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
B	IPR016713	Poly(A) polymerase complex subunit Air1/2, budding yeast	Family
B	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
B	IPR001878	Zinc finger, CCHC-type	Domain
B	IPR051644	TRAMP complex component and AT-rich DNA-binding protein	Family
B	IPR049024	AIR2-like, CCHC-type 1 zinc finger 4	Conserved Site
A	IPR054708	Poly(A) RNA polymerase, mitochondrial-like, central palm domain	Domain
A	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
A	IPR045862	Nucleotidyltransferase Trf4-like	Family
A	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.