2LLI | pdb_00002lli

Low resolution structure of RNA-binding subunit of the TRAMP complex

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e2lliA3	A: Bromodomain-containing protein 4 ET domain	X: Bromodomain-containing protein 4 ET domain	H: Bromodomain-containing protein 4 ET domain	T: STI1-HOP_DP	F:	ECOD (20:10:01)
A		e2lliA1	A: Outer membrane meander beta-barrels	X: Porins	H: Porin	T: AIR2-like_ZnK4	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
A	PF21759	AIR2-like, CCHC-type 1 zinc finger 4 (AIR2-like_ZnK4)	AIR2-like, CCHC-type 1 zinc finger 4	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016713	Poly(A) polymerase complex subunit Air1/2, budding yeast	Family
A	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A	IPR001878	Zinc finger, CCHC-type	Domain
A	IPR051644	TRAMP complex component and AT-rich DNA-binding protein	Family
A	IPR049024	AIR2-like, CCHC-type 1 zinc finger 4	Conserved Site

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.