3VQT

Crystal structure analysis of the translation factor RF3

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-G C-terminal domain-like	8092485	3001287	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8092487	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8092486	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-G C-terminal domain-like	8092484	3001287	SCOP2B (2022-06-29)
B	SCOP2 Family	RF3 C-terminal domain-like	8045935	4004772	SCOP2 (2022-06-29)
B	SCOP2 Family	Translation factor common region-like	8092483	4004050	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	EF-G C-terminal domain-like	8092484	3001287	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	EF-G C-terminal domain-like	8092485	3001287	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ras-like P-loop GTPases	8092486	3002022	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	EF-Tu post-G domain-like	8092487	3002024	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	EF-G C-terminal domain-like	8092485	3001287	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-Tu post-G domain-like	8092487	3002024	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-G C-terminal domain-like	8092484	3001287	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8092486	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EF-Tu post-G domain-like	8092487	3002024	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EF-G C-terminal domain-like	8092484	3001287	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	EF-G C-terminal domain-like	8092485	3001287	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8092486	3002022	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	e3vqtA9	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
A	UNK_F_TYPE	e3vqtA8	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: UNK_F_TYPE	ECOD (1.6)
A	MnmE_helical_2nd	e3vqtA7	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)
B	GTP_EFTU_D2	e3vqtB5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
B	UNK_F_TYPE	e3vqtB4	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: UNK_F_TYPE	ECOD (1.6)
B	MnmE_helical_2nd	e3vqtB3	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)
C	GTP_EFTU_D2	e3vqtC5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
C	UNK_F_TYPE	e3vqtC4	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: UNK_F_TYPE	ECOD (1.6)
C	MnmE_helical_2nd	e3vqtC3	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)
D	GTP_EFTU_D2	e3vqtD5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2	ECOD (1.6)
D	UNK_F_TYPE	e3vqtD4	A: a+b two layers	X: Alpha-beta plaits	H: EF-G C-terminal domain-like (From Topology)	T: EF-G C-terminal domain-like	F: UNK_F_TYPE	ECOD (1.6)
D	MnmE_helical_2nd	e3vqtD3	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.30.70.3280	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Peptide chain release factor 3, domain III	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.30.70.3280	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Peptide chain release factor 3, domain III	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.30.70.3280	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Peptide chain release factor 3, domain III	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.30.70.3280	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Peptide chain release factor 3, domain III	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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
A, B, C, D	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	PF16658	Class II release factor RF3, C-terminal domain (RF3_C)	Class II release factor RF3, C-terminal domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Peptide chain release factor 3	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 guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide 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 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 regulation of cellular component organization cellular biosynthetic process organonitrogen compound biosynthetic process protein-containing complex disassembly regulation of protein-containing complex disassembly regulation of primary metabolic process cellular component organization post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process translational termination cellular component organization or biogenesis regulation of cellular process regulation of cellular component organization cellular biosynthetic process organonitrogen compound biosynthetic process protein-containing complex disassembly regulation of protein-containing complex disassembly regulation of primary metabolic process cellular component organization post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process translational termination cellular component organization or biogenesis regulation of biosynthetic process cellular component disassembly regulation of biological process organonitrogen compound metabolic process protein-containing complex organization cellular metabolic process regulation of protein metabolic process regulation of translational termination biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR032090	Peptide chain release factor 3, C-terminal	Domain
A, B, C, D	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A, B, C, D	IPR041732	Peptide chain release factor 3, GTP-binding domain	Domain
A, B, C, D	IPR031157	Tr-type G domain, conserved site	Conserved Site
A, B, C, D	IPR035647	EF-G domain III/V-like	Homologous Superfamily
A, B, C, D	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A, B, C, D	IPR004548	Peptide chain release factor 3	Family
A, B, C, D	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, B, C, D	IPR005225	Small GTP-binding protein domain	Domain
A, B, C, D	IPR038467	Peptide chain release factor 3, domain III superfamily	Homologous Superfamily
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.