2VGN

Structure of S. cerevisiae Dom34, a translation termination-like factor involved in RNA quality control pathways and interacting with Hbs1 (SelenoMet-labeled protein)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2vgna1	All beta proteins	Sm-like fold	Dom34/Pelota N-terminal domain-like	Dom34/Pelota N-terminal domain-like	Dom34	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d2vgna2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Translational machinery components	ERF1/Dom34 middle domain-like	Dom34	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d2vgna3	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	L30e-like	ERF1/Dom34 C-terminal domain-like	Dom34	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d2vgnb1	All beta proteins	Sm-like fold	Dom34/Pelota N-terminal domain-like	Dom34/Pelota N-terminal domain-like	Dom34	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d2vgnb2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Translational machinery components	ERF1/Dom34 middle domain-like	Dom34	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d2vgnb3	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	L30e-like	ERF1/Dom34 C-terminal domain-like	Dom34	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Dom34/Pelota N-terminal domain-like	8025084	4001709	SCOP2 (2022-06-29)
A	SCOP2 Family	ERF1/Dom34 C-terminal domain-like	8025088	4001517	SCOP2 (2022-06-29)
A	SCOP2 Family	ERF1/Dom34 middle domain-like	8025085	4000556	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Dom34/Pelota N-terminal domain-like	8037463	3000284	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	L30e-like	8037467	3001739	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Translational machinery components	8037464	3000571	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	L30e-like	8037467	3001739	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Translational machinery components	8037464	3000571	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Dom34/Pelota N-terminal domain-like	8037463	3000284	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)
A	PF03463	e2vgnA1	A: beta barrels	X: SH3	H: Dom34/Pelota N-terminal domain-like (From Topology)	T: Dom34/Pelota N-terminal domain-like	F: PF03463	ECOD (1.6)
A	PF03465	e2vgnA2	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: PF03465	ECOD (1.6)
A	PF03464	e2vgnA3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF03464	ECOD (1.6)
B	PF03463	e2vgnB1	A: beta barrels	X: SH3	H: Dom34/Pelota N-terminal domain-like (From Topology)	T: Dom34/Pelota N-terminal domain-like	F: PF03463	ECOD (1.6)
B	PF03465	e2vgnB2	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: PF03465	ECOD (1.6)
B	PF03464	e2vgnB3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF03464	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.870	Mainly Beta	Roll	SH3 type barrels.	Pelota, domain A	CATH (4.3.0)
A	3.30.420.60	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
B	2.30.30.870	Mainly Beta	Roll	SH3 type barrels.	Pelota, domain A	CATH (4.3.0)
B	3.30.420.60	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03465	eRF1 domain 3 (eRF1_3)	eRF1 domain 3	The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The o ...	The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site [1]. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.	Domain
A, B	PF03463	eRF1 domain 1 (eRF1_1)	eRF1 domain 1	The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The o ...	The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site [1]. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.	Domain
A, B	PF03464	eRF1 domain 2 (eRF1_2)	eRF1 domain 2	The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The o ...	The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known [1]. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site [1]. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DOM34	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process regulation of cellular process cellular biosynthetic process positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process catabolic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process mRNA catabolic process nuclear-transcribed mRNA catabolic process negative regulation of metabolic process nuclear-transcribed mRNA catabolic process, non-stop decay mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process organic cyclic compound metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process organic substance catabolic process nonfunctional rRNA decay rRNA catabolic process ncRNA metabolic process rRNA metabolic process rescue of stalled ribosome cellular component organization organelle disassembly cellular component organization or biogenesis cellular component disassembly ribosome disassembly organelle organization translational elongation cell division nuclear-transcribed mRNA catabolic process, no-go decay translational initiation regulation of translational initiation positive regulation of translational initiation sexual reproduction reproductive process meiotic cell cycle cell cycle RNA surveillance	protein-containing complex Dom34-Hbs1 complex intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR005141	eRF1 domain 2	Domain
A, B	IPR004405	Translation release factor pelota	Family
A, B	IPR005140	eRF1 domain 1/Pelota-like	Domain
A, B	IPR042226	eRF1, domain 2 superfamily	Homologous Superfamily
A, B	IPR038069	Pelota/DOM34, N-terminal domain	Homologous Superfamily
A, B	IPR005142	eRF1 domain 3	Domain
A, B	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.