3E20 | pdb_00003e20

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)
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)
C [auth D]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056490	3002024	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056489	3002024	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth H]		e3e20H1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: RA	F:	ECOD (20:10:01)
F [auth H]		e3e20H2	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T:	F:	ECOD (20:10:01)
H [auth K]		e3e20K1	A: MHC antigen-recognition domain	X: MHC antigen-recognition domain	H: MHC antigen-recognition domain	T: Glyco_hydro_35	F:	ECOD (20:10:01)
D [auth B]		e3e20B1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Ras	F:	ECOD (20:10:01)
D [auth B]		e3e20B3	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T:	F:	ECOD (20:10:01)
B [auth C]		e3e20C1	A: Alpha-beta plaits	X: Nucleotide-diphospho-sugar transferases	H: Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	T: DsbD_N	F:	ECOD (20:10:01)
E		e3e20E1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Ras	F:	ECOD (20:10:01)
G [auth J]		e3e20J1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Ras	F:	ECOD (20:10:01)
C [auth D]		e3e20D1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Ras	F:	ECOD (20:10:01)
A		e3e20A1	A: OB-fold	X: Nucleic acid-binding protein	H: Nucleic acid-binding protein	T: MerR_1	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)
C [auth D]	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 factor activity translation release factor activity translation termination factor activity GTPase regulator activity enzyme regulator activity nucleoside-triphosphatase regulator activity molecular function regulator activity RNA binding binding sequence-specific mRNA binding nucleic acid 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-containing complex cellular anatomical structure intracellular anatomical structure translation release factor complex cytoplasm cytosol
A, C [auth D], E, G [auth J]	Eukaryotic peptide chain release factor GTP-binding subunit	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding translation factor activity translation release factor activity translation termination factor activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding translation factor activity translation release factor activity translation termination factor activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide 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	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 regulation of cellular process negative regulation of biological 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 negative regulation of metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA 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 positive 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 positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process	protein-containing complex cellular anatomical structure intracellular anatomical structure translation release factor complex cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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]	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]	IPR005140	eRF1/Pelota-like, N-terminal domain	Domain
B [auth C], D [auth B], F [auth H], H [auth K]	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily
A, C [auth D], E, G [auth J]	IPR050100	Translation factor GTPase superfamily members	Family
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]	IPR054696	GTP-eEF1A, C-terminal domain	Domain
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]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.