3E1Y | pdb_00003e1y

Crystal structure of human eRF1/eRF3 complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Translational machinery components	8044552	3000571	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Translational machinery components	8044552	3000571	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Translational machinery components	8044552	3000571	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1	8035419	3001963	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Translational machinery components	8044552	3000571	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1	8035419	3001963	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)
H	GTP_EFTU_D2_1	e3e1yH1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
H	GTP_EFTU_D3_1	e3e1yH2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3_1	ECOD (1.6)
G	GTP_EFTU_D2_1	e3e1yG1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
G	GTP_EFTU_D3_1	e3e1yG2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3_1	ECOD (1.6)
F	GTP_EFTU_D2_1	e3e1yF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
F	GTP_EFTU_D3_1	e3e1yF2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3_1	ECOD (1.6)
E	GTP_EFTU_D2_1	e3e1yE2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
E	GTP_EFTU_D3_1	e3e1yE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3_1	ECOD (1.6)
D	eRF1_3	e3e1yD8	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: eRF1_3	ECOD (1.6)
D	eRF1_1_1	e3e1yD7	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: eRF1_1_1	ECOD (1.6)
D	eRF1_2	e3e1yD9	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: eRF1_2	ECOD (1.6)
C	eRF1_3	e3e1yC8	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: eRF1_3	ECOD (1.6)
C	eRF1_1_1	e3e1yC7	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: eRF1_1_1	ECOD (1.6)
C	eRF1_2	e3e1yC9	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: eRF1_2	ECOD (1.6)
B	eRF1_3	e3e1yB4	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: eRF1_3	ECOD (1.6)
B	eRF1_1_1	e3e1yB1	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: eRF1_1_1	ECOD (1.6)
B	eRF1_2	e3e1yB2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: eRF1_2	ECOD (1.6)
A	eRF1_3	e3e1yA4	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: eRF1_3	ECOD (1.6)
A	eRF1_1_1	e3e1yA1	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: eRF1_1_1	ECOD (1.6)
A	eRF1_2	e3e1yA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: eRF1_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
G	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
F	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
E	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
D	3.30.420.60	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.30.420.60	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.960.10	Alpha Beta	2-Layer Sandwich	Translation, Eukaryotic Peptide Chain Release Factor Subunit 1	Chain 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)
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
E, F, G, H	PF22594	GTP-eEF1A C-terminal domain-like (GTP-eEF1A_C)	GTP-eEF1A C-terminal domain-like	This entry represents a beta-barrel domain that is found C-terminal in homologues of elongation factor eEF1A.	Domain
E, F, G, H	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain
A, B, C, D	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, C, D	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, C, D	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
E, F, G, H	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A	translation factor activity translation release factor activity translation termination factor activity RNA binding binding nucleic acid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding translation factor activity translation release factor activity translation termination factor activity RNA binding binding nucleic acid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	mitotic cell cycle process cellular process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process protein methylation primary metabolic process macromolecule methylation protein alkylation methylation mitotic cell cycle process cellular process cell cycle phase transition cell cycle G1/S transition of mitotic cell cycle cell cycle G1/S phase transition mitotic cell cycle mitotic cell cycle phase transition cell cycle process protein methylation primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification metabolic process protein metabolic process macromolecule metabolic process protein modification process cellular component disassembly protein-containing complex organization protein-containing complex disassembly translation gene expression protein biosynthetic process macromolecule biosynthetic process cellular component organization biosynthetic process translational termination cellular component organization or biogenesis 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 macromolecule metabolic 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 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 nucleic acid metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol protein-containing complex translation release factor complex
A, B, C, D	Eukaryotic peptide chain release factor subunit 1	translation release factor activity, codon specific translation factor activity translation release factor activity translation termination factor activity ribonucleoprotein complex binding protein-containing complex binding binding ribosome binding 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 translation release factor activity, codon specific translation factor activity translation release factor activity translation termination factor activity ribonucleoprotein complex binding protein-containing complex binding binding ribosome binding 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 peptidyl-tRNA hydrolase activity catalytic activity RNA binding nucleic acid binding sequence-specific mRNA binding mRNA binding	cellular component disassembly cytoplasmic translational termination protein-containing complex organization protein-containing complex disassembly primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process cellular component organization biosynthetic process cytoplasmic translation cellular process metabolic process cellular component disassembly cytoplasmic translational termination protein-containing complex organization protein-containing complex disassembly primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process cellular component organization biosynthetic process cytoplasmic translation cellular process metabolic process translational termination cellular component organization or biogenesis protein 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 macromolecule metabolic 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 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 nucleic acid metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure cytosolic ribosome organelle membraneless organelle intracellular membraneless organelle ribosome cytoplasm cytosol protein-containing complex translation release factor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR050100	Translation factor GTPase superfamily members	Family
E, F, G, H	IPR000795	Translational (tr)-type GTP-binding domain	Domain
E, F, G, H	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
E, F, G, H	IPR031157	Tr-type G domain, conserved site	Conserved Site
E, F, G, H	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
E, F, G, H	IPR054696	GTP-eEF1A, C-terminal domain	Domain
E, F, G, H	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
E, F, G, H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR004403	Peptide chain release factor eRF1/aRF1	Family
A, B, C, D	IPR005141	eRF1 domain 2	Domain
A, B, C, D	IPR042226	eRF1, domain 2 superfamily	Homologous Superfamily
A, B, C, D	IPR024049	eRF1, domain 1	Homologous Superfamily
A, B, C, D	IPR005142	eRF1 domain 3	Domain
A, B, C, D	IPR005140	eRF1/Pelota-like, N-terminal domain	Domain
A, B, C, D	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F, G, H	Pharos: P15170	pancreatic ductal adenocarcinoma Pick disease psoriasis tuberculosis adenoma cystic fibrosis glioblastoma large cell medulloblastoma malignant ependymoma myopathy osteosarcoma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma Sjogren syndrome astrocytic tumor pancreatic ductal adenocarcinoma Pick disease psoriasis tuberculosis adenoma cystic fibrosis glioblastoma large cell medulloblastoma malignant ependymoma myopathy osteosarcoma pancreatic intraductal papillary-mucinous carcinoma plasma cell myeloma Sjogren syndrome astrocytic tumor ductal breast carcinoma in situ hereditary spastic paraplegia lung adenocarcinoma malignant glioma non-small cell lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia progressive supranuclear palsy testicular germ cell tumor breast carcinoma gastric carcinoma invasive ductal breast carcinoma lung cancer medulloblastoma oligodendroglioma
A, B, C, D	Pharos: P62495	autism spectrum disorder myopathy breast cancer ovarian cancer diabetes mellitus plasma cell myeloma