3IZQ

Structure of the Dom34-Hbs1-GDPNP complex bound to a translating ribosome

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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 [auth 0]	SCOP2B Superfamily	L30e-like	8037467	3001739	SCOP2B (2022-06-29)
A [auth 0]	SCOP2B Superfamily	Dom34/Pelota N-terminal domain-like	8037463	3000284	SCOP2B (2022-06-29)
A [auth 0]	SCOP2B Superfamily	Translational machinery components	8037464	3000571	SCOP2B (2022-06-29)
B [auth 1]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056492	3002024	SCOP2B (2022-06-29)
B [auth 1]	SCOP2B Superfamily	Ras-like P-loop GTPases	8056491	3002022	SCOP2B (2022-06-29)
B [auth 1]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056493	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 [auth 0]	eRF1_1	e3izq02	A: beta barrels	X: SH3	H: Dom34/Pelota N-terminal domain-like (From Topology)	T: Dom34/Pelota N-terminal domain-like	F: eRF1_1	ECOD (1.6)
A [auth 0]	eRF1_3	e3izq03	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 [auth 0]	eRF1_2	e3izq01	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 [auth 1]	GTP_EFTU_D2_1	e3izq12	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
B [auth 1]	GTP_EFTU_D3_1	e3izq13	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 1]	HBS1_N	e3izq14	A: alpha arrays	X: RuvA-C	H: RuvA-C, UBA, CRAL/TRIO-N, HBS1 (From Topology)	T: RuvA-C, UBA, CRAL/TRIO-N, HBS1	F: HBS1_N	ECOD (1.6)
B [auth 1]	MnmE_helical_2nd	e3izq11	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth 0]	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 [auth 0]	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 [auth 0]	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
B [auth 1]	PF00009	Elongation factor Tu GTP binding domain (GTP_EFTU)	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	Domain
B [auth 1]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth 0]	Protein 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 positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule 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 catabolic process 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 nuclear-transcribed mRNA catabolic process, non-stop decay 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 nonfunctional rRNA decay rRNA catabolic process rRNA metabolic process cellular component disassembly ribosome disassembly rescue of stalled ribosome cellular component organization organelle organization organelle disassembly translational elongation cellular component organization or biogenesis 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 cellular anatomical structure intracellular anatomical structure cytoplasm
B [auth 1]	Elongation factor 1 alpha-like protein	translation factor activity translation elongation factor activity translation factor activity, RNA binding 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 translation factor activity translation elongation factor activity translation factor activity, RNA binding 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	regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule 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 nonfunctional rRNA decay catabolic process RNA metabolic process rRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process rRNA metabolic process RNA catabolic process cellular component disassembly ribosome disassembly rescue of stalled ribosome cellular component organization organelle organization organelle disassembly translational elongation cellular component organization or biogenesis negative regulation of biological process negative regulation of cellular 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 gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nuclear-transcribed mRNA catabolic process, no-go decay translational initiation regulation of translational initiation positive regulation of translational initiation	protein-containing complex Dom34-Hbs1 complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth 0]	IPR005141	eRF1 domain 2	Domain
A [auth 0]	IPR004405	Translation release factor pelota	Family
A [auth 0]	IPR005140	eRF1 domain 1/Pelota-like	Domain
A [auth 0]	IPR042226	eRF1, domain 2 superfamily	Homologous Superfamily
A [auth 0]	IPR038069	Pelota/DOM34, N-terminal domain	Homologous Superfamily
A [auth 0]	IPR005142	eRF1 domain 3	Domain
A [auth 0]	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily
B [auth 1]	IPR050100	Translation factor GTPase superfamily members	Family
B [auth 1]	IPR000795	Translational (tr)-type GTP-binding domain	Domain
B [auth 1]	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
B [auth 1]	IPR031157	Tr-type G domain, conserved site	Conserved Site
B [auth 1]	IPR054696	GTP-eEF1A, C-terminal domain	Domain
B [auth 1]	IPR015033	HBS1-like protein, N-terminal	Domain
B [auth 1]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
B [auth 1]	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.