8ASW | pdb_00008asw

Cryo-EM structure of yeast Elp123 in complex with alanine tRNA

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF04055	Radical SAM superfamily (Radical_SAM)	Radical SAM superfamily	Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.	Domain
C	PF16199	Radical_SAM C-terminal domain (Radical_SAM_C)	Radical_SAM C-terminal domain	-	Family
C	PF00583	Acetyltransferase (GNAT) family (Acetyltransf_1)	Acetyltransferase (GNAT) family	-	Family
C	PF23613	ELP3 N-terminal domain (ELP3_N)	ELP3 N-terminal domain	This domain is found N-terminal in the human Elongator complex protein 3 (ELP3) and related proteins. This protein is required for multiple modifications of tRNA. In the elongation complex, it acts as a tRNA uridine(34) acetyltransferase. It may also ...	This domain is found N-terminal in the human Elongator complex protein 3 (ELP3) and related proteins. This protein is required for multiple modifications of tRNA. In the elongation complex, it acts as a tRNA uridine(34) acetyltransferase. It may also act as a lysine acetyltransferase by mediating acetylation of target proteins [1]. The domain represented by this entry is predicted to fold into a globular structure consisting of two nearly orthogonal alpha-helical hairpins.	Domain
B	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
A, D	PF23797	ELP1 N-terminal second beta-propeller (Beta-prop_ELP1_2nd)	ELP1 N-terminal second beta-propeller	-	Repeat
A, D	PF23936	ELP1 three-helix bundle (HB_ELP1)	ELP1 three-helix bundle	This entry represents the helical bundle domain found within the C-terminal dimerization domain of Elongator complex protein 1 (ELP1), from eukaryotes. Elongator is a conserved protein complex implicated in multiple processes including regulation of ...	This entry represents the helical bundle domain found within the C-terminal dimerization domain of Elongator complex protein 1 (ELP1), from eukaryotes. Elongator is a conserved protein complex implicated in multiple processes including regulation of transcription, alpha-tubulin acetylation and tRNA modification. Mutations in the ELP1 gene have been shown to cause the neurodegenerative disease familial dysautonomia [1]. The C-terminal dimerization domain consists of 28 alpha-helices organised in three domains: an elongated alpha-solenoid domain (helices 1 to 14); a TPR domain, formed by six double-helix repeats (helices 15 to 26); and a three-helix bundle, C-terminal cap (helices 26 to 28) [2]. ELP1 self-association contributes to its stability and is important for Elongator assembly [2]. ELP1 is considered to function both as a scaffold, for Elongator complex ELP2 and ELP3 binding, and as a docking site for various factors that regulate Elongator activity [2-4]. Also known as IKAP, ELP1 acts as a regulator of IkB kinase complex involved in proinflammatory cytokine signalling [5].	Domain
A, D	PF04762	ELP1 first N-terminal beta-propeller (Beta-prop_ELP1_1st)	ELP1 first N-terminal beta-propeller	-	Repeat
A, D	PF23925	ELP1 alpha-solenoid (A-sol_ELP1)	ELP1 alpha-solenoid	-	Repeat
A, D	PF23878	ELP1 TPR domain (TPR_ELP1)	ELP1 TPR domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth X]	Alanine tRNA	-	-	-
C	Elongator complex protein 3	acetyltransferase activity acyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity tRNA uridine(34) acetyltransferase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding acetyltransferase activity acyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity tRNA uridine(34) acetyltransferase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding RNA binding tRNA binding nucleic acid binding cation binding ion binding metal ion binding	tRNA modification RNA metabolic process primary metabolic process tRNA wobble uridine modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing tRNA modification RNA metabolic process primary metabolic process tRNA wobble uridine modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation tRNA wobble base modification metabolic process cellular process macromolecule metabolic process RNA processing regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process translation protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process protein metabolic process regulation of metabolic process	protein-containing complex catalytic complex elongator holoenzyme complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm protein-containing complex catalytic complex elongator holoenzyme complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
B	Elongator complex protein 2	cytoskeletal protein binding microtubule binding protein binding binding tubulin binding	primary metabolic process protein urmylation macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal localization establishment of protein localization protein transport primary metabolic process protein urmylation macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization tRNA modification RNA metabolic process tRNA wobble uridine modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing tRNA wobble base modification RNA processing regulation of cellular process regulation of primary metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II 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 regulation of protein metabolic process translation protein biosynthetic process post-transcriptional regulation of gene expression regulation of translation	protein-containing complex catalytic complex elongator holoenzyme complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm protein-containing complex catalytic complex elongator holoenzyme complex intracellular protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
A, D	Elongator complex protein 1	RNA binding binding tRNA binding nucleic acid binding identical protein binding protein binding	tRNA modification RNA metabolic process primary metabolic process tRNA wobble uridine modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing tRNA modification RNA metabolic process primary metabolic process tRNA wobble uridine modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing macromolecule modification tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation tRNA wobble base modification metabolic process cellular process macromolecule metabolic process RNA processing localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization regulation of cellular process regulation of primary metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II 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 regulation of protein metabolic process translation protein biosynthetic process post-transcriptional regulation of gene expression regulation of translation protein metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex elongator holoenzyme complex intracellular protein-containing complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex elongator holoenzyme complex intracellular protein-containing complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR007197	Radical SAM	Domain
C	IPR034687	Elongator complex protein 3-like	Family
C	IPR006638	Elp3/MiaA/NifB-like, radical SAM core domain	Domain
C	IPR032432	Radical SAM, C-terminal extension	Domain
C	IPR000182	GNAT domain	Domain
C	IPR058240	Radical SAM superfamily	Homologous Superfamily
C	IPR016181	Acyl-CoA N-acyltransferase	Homologous Superfamily
C	IPR056591	ELP3-like, N-terminal domain	Domain
C	IPR039661	ELP3/YhcC	Family
B	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B	IPR001680	WD40 repeat	Repeat
B	IPR037289	Elongator complex protein 2	Family
B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, D	IPR056167	ELP1, alpha-solenoid	Domain
A, D	IPR006849	Elongator complex protein 1	Family
A, D	IPR056169	ELP1, three-helical bundle	Domain
A, D	IPR056166	ELP1, TPR domain	Domain
A, D	IPR056165	ELP1, N-terminal second beta-propeller	Domain
A, D	IPR056164	ELP1, first N-terminal beta-propeller	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.