1DT9

THE CRYSTAL STRUCTURE OF HUMAN EUKARYOTIC RELEASE FACTOR ERF1-MECHANISM OF STOP CODON RECOGNITION AND PEPTIDYL-TRNA HYDROLYSIS

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1dt9a1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Translational machinery components	ERF1/Dom34 middle domain-like	Middle domain of eukaryotic peptide chain release factor subunit 1, ERF1	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1dt9a2	Alpha and beta proteins (a+b)	Bacillus chorismate mutase-like	L30e-like	ERF1/Dom34 C-terminal domain-like	C-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1dt9a3	Alpha and beta proteins (a+b)	N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1	N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1	N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1	N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	ERF1/Dom34 C-terminal domain-like	8023650	4001517	SCOP2 (2022-06-29)
A	SCOP2 Family	ERF1/Dom34 middle domain-like	8032174	4000556	SCOP2 (2022-06-29)
A	SCOP2 Family	N-terminal domain of eukaryotic peptide chain release factor subunit 1 ERF1	8023039	4001605	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	L30e-like	8036030	3001739	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Translational machinery components	8044552	3000571	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	N-terminal domain of eukaryotic peptide chain release factor subunit 1 ERF1	8035419	3001963	SCOP2 (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	PF03465	e1dt9A2	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: PF03465	ECOD (1.6)
A	PF03463	e1dt9A1	A: a+b three layers	X: N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 (From Topology)	H: N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 (From Topology)	T: N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1	F: PF03463	ECOD (1.6)
A	PF03464	e1dt9A3	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	3.30.960.10	Alpha Beta	2-Layer Sandwich	Translation, Eukaryotic Peptide Chain Release Factor Subunit 1	Chain 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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	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	PROTEIN (EUKARYOTIC PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1)	translation release factor activity, codon specific translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation release factor activity nucleic acid binding translation termination factor activity translation factor activity, RNA binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding aminoacyl-tRNA hydrolase activity hydrolase activity, acting on ester bonds translation release factor activity, codon specific translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation release factor activity nucleic acid binding translation termination factor activity translation factor activity, RNA binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding aminoacyl-tRNA hydrolase activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid carboxylic ester hydrolase activity hydrolase activity catalytic activity, acting on a tRNA catalytic activity RNA binding sequence-specific mRNA binding mRNA binding	cytoplasmic translational termination cellular biosynthetic process organonitrogen compound biosynthetic process protein-containing complex disassembly cellular component organization organic substance metabolic process organic substance biosynthetic process translational termination cellular component organization or biogenesis protein metabolic process cellular component disassembly organonitrogen compound metabolic process protein-containing complex organization cellular metabolic process cytoplasmic translational termination cellular biosynthetic process organonitrogen compound biosynthetic process protein-containing complex disassembly cellular component organization organic substance metabolic process organic substance biosynthetic process translational termination cellular component organization or biogenesis protein metabolic process cellular component disassembly organonitrogen compound metabolic process protein-containing complex organization cellular metabolic process primary metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process cytoplasmic translation cellular process metabolic process macromolecule metabolic process protein methylation macromolecule methylation protein alkylation methylation macromolecule modification protein modification process regulation of cellular process regulation of cellular component organization regulation of protein-containing complex disassembly regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of biosynthetic process regulation of biological process regulation of protein metabolic process regulation of translational termination biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process regulation of metabolic process catabolic process nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 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 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	intracellular organelle intracellular anatomical structure cytosolic ribosome organelle intracellular non-membrane-bounded organelle ribosome cytoplasm cellular anatomical entity cytosol non-membrane-bounded organelle protein-containing complex translation release factor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004403	Peptide chain release factor eRF1/aRF1	Family
A	IPR005141	eRF1 domain 2	Domain
A	IPR005140	eRF1 domain 1/Pelota-like	Domain
A	IPR042226	eRF1, domain 2 superfamily	Homologous Superfamily
A	IPR024049	eRF1, domain 1	Homologous Superfamily
A	IPR005142	eRF1 domain 3	Domain
A	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P62495	autism spectrum disorder myopathy breast cancer ovarian cancer diabetes mellitus plasma cell myeloma

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.