3E20

Crystal structure of S.pombe 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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8056490	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8056489	3002024	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056489	3002024	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056490	3002024	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	EF-Tu post-G domain-like	8056489	3002024	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	EF-Tu post-G domain-like	8056490	3002024	SCOP2B (2022-06-29)
G [auth J]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056490	3002024	SCOP2B (2022-06-29)
G [auth J]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056489	3002024	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	GTP_EFTU_D2_1	e3e20A2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
A	GTP_EFTU_D3_1	e3e20A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3_1	ECOD (1.6)
C [auth D]	GTP_EFTU_D2_1	e3e20D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
C [auth D]	GTP_EFTU_D3_1	e3e20D2	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	e3e20E1	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	e3e20E2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3_1	ECOD (1.6)
G [auth J]	GTP_EFTU_D2_1	e3e20J1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
G [auth J]	GTP_EFTU_D3_1	e3e20J2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3_1	ECOD (1.6)
B [auth C]	eRF1_3	e3e20C2	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 [auth C]	eRF1_1_1	e3e20C1	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 [auth B]	eRF1_3	e3e20B3	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 [auth B]	eRF1_1_1	e3e20B1	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)
F [auth H]	eRF1_3	e3e20H1	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: eRF1_3	ECOD (1.6)
F [auth H]	eRF1_1_1	e3e20H2	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)
H [auth K]	eRF1_3	e3e20K2	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: eRF1_3	ECOD (1.6)
H [auth K]	eRF1_1_1	e3e20K1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C [auth D]	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)
G [auth J]	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B [auth C]	3.30.960.10	Alpha Beta	2-Layer Sandwich	Translation, Eukaryotic Peptide Chain Release Factor Subunit 1	Chain A	CATH (4.3.0)
B [auth C]	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
D [auth B]	3.30.960.10	Alpha Beta	2-Layer Sandwich	Translation, Eukaryotic Peptide Chain Release Factor Subunit 1	Chain A	CATH (4.3.0)
D [auth B]	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
F [auth H]	6.10.140.2070	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
F [auth H]	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
H [auth K]	6.10.140.2070	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
H [auth K]	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, C [auth D], E, G [auth J]	PF03143	Elongation factor Tu C-terminal domain (GTP_EFTU_D3)	Elongation factor Tu C-terminal domain	Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA [1] and binding to EF-Ts Pfam:PF00889 [2].	Domain
B [auth C], D [auth B], F [auth H], H [auth K]	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
B [auth C], D [auth B], F [auth H], H [auth K]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth D], E, G [auth J]	Eukaryotic peptide chain release factor GTP-binding subunit	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 guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding 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 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	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 regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process regulation of metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process positive regulation of biological process RNA metabolic process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process regulation of biosynthetic process RNA destabilization nuclear-transcribed mRNA catabolic process biological regulation regulation of macromolecule metabolic process regulation of catabolic process mRNA metabolic process nucleic acid metabolic process organic cyclic compound catabolic process regulation of cellular biosynthetic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process negative regulation of biosynthetic process regulation of RNA stability regulation of mRNA metabolic process organic substance catabolic process	protein-containing complex intracellular anatomical structure translation release factor complex cytoplasm cellular anatomical entity cytosol
B [auth C], D [auth B], F [auth H], H [auth K]	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 GTPase regulator activity enzyme regulator activity nucleoside-triphosphatase regulator activity molecular function regulator activity RNA binding 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 GTPase regulator activity enzyme regulator activity nucleoside-triphosphatase regulator activity molecular function regulator 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-containing complex intracellular anatomical structure translation release factor complex cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth D], E, G [auth J]	IPR003285	Eukaryotic peptide chain release factor GTP-binding subunit	Family
A, C [auth D], E, G [auth J]	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A, C [auth D], E, G [auth J]	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
A, C [auth D], E, G [auth J]	IPR031157	Tr-type G domain, conserved site	Conserved Site
A, C [auth D], E, G [auth J]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, C [auth D], E, G [auth J]	IPR004160	Translation elongation factor EFTu/EF1A, C-terminal	Domain
A, C [auth D], E, G [auth J]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth C], D [auth B], F [auth H], H [auth K]	IPR004403	Peptide chain release factor eRF1/aRF1	Family
B [auth C], D [auth B], F [auth H], H [auth K]	IPR005141	eRF1 domain 2	Domain
B [auth C], D [auth B], F [auth H], H [auth K]	IPR005140	eRF1 domain 1/Pelota-like	Domain
B [auth C], D [auth B], F [auth H], H [auth K]	IPR042226	eRF1, domain 2 superfamily	Homologous Superfamily
B [auth C], D [auth B], F [auth H], H [auth K]	IPR024049	eRF1, domain 1	Homologous Superfamily
B [auth C], D [auth B], F [auth H], H [auth K]	IPR005142	eRF1 domain 3	Domain
B [auth C], D [auth B], F [auth H], H [auth K]	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.