6JI2

Crystal structure of archaeal ribosomal protein aP1, aPelota, and GTP-bound aEF1A 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	8056523	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8056521	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8056520	3002022	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	Ras-like P-loop GTPases	8056520	3002022	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056523	3002024	SCOP2B (2022-06-29)
C [auth E]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056521	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	e6ji2A2	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	e6ji2A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GTP_EFTU_D3_1	ECOD (1.6)
A	MnmE_helical_2nd	e6ji2A3	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 [auth E]	GTP_EFTU_D2_1	e6ji2E2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_1	ECOD (1.6)
C [auth E]	GTP_EFTU_D3_1	e6ji2E1	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 E]	MnmE_helical_2nd	e6ji2E3	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	eRF1_1	e6ji2B2	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)
B	eRF1_3	e6ji2B3	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_2	e6ji2B1	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)
D [auth F]	eRF1_1	e6ji2F3	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)
D [auth F]	eRF1_3	e6ji2F2	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 F]	eRF1_2	e6ji2F1	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)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
C [auth E]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
C [auth E]	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
B	2.30.30.870	Mainly Beta	Roll	SH3 type barrels.	Pelota, domain A	CATH (utative)
B	3.30.420.60	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
B	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (utative)
D [auth F]	2.30.30.870	Mainly Beta	Roll	SH3 type barrels.	Pelota, domain A	CATH (utative)
D [auth F]	3.30.420.60	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
D [auth F]	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth E]	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, C [auth E]	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
A, C [auth E]	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
B, D [auth F]	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, D [auth F]	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 E]	Elongation factor 1-alpha	translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding 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 translation regulator activity binding organic cyclic compound binding translation regulator activity, nucleic acid binding translation elongation factor activity nucleic acid binding 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	cellular metabolic process sulfur compound metabolic process metabolic process cellular process	intracellular anatomical structure cytoplasm cellular anatomical entity
B, D [auth F]	Protein pelota homolog	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation nuclear-transcribed mRNA catabolic process, non-stop decay regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process nonfunctional rRNA decay rRNA catabolic process rRNA metabolic process nuclear-transcribed mRNA catabolic process, no-go decay cellular component organization cellular component disassembly organelle organization organelle disassembly ribosome disassembly cellular component organization or biogenesis RNA surveillance	intracellular anatomical structure cytoplasm cellular anatomical entity
E [auth X]	Archaeal ribosomal stalk protein aP1	structural molecule activity structural constituent of ribosome	cellular biosynthetic process cellular metabolic process primary metabolic process translation gene expression macromolecule biosynthetic process biosynthetic process translational elongation metabolic process cellular process macromolecule metabolic process protein metabolic process	protein-containing complex ribonucleoprotein complex intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle ribosome cellular anatomical entity non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth E]	IPR005225	Small GTP-binding domain	Domain
A, C [auth E]	IPR050100	Translation factor GTPase superfamily members	Family
A, C [auth E]	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A, C [auth E]	IPR009001	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal	Homologous Superfamily
A, C [auth E]	IPR031157	Tr-type G domain, conserved site	Conserved Site
A, C [auth E]	IPR004539	Translation elongation factor EF1A, eukaryotic/archaeal	Family
A, C [auth E]	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A, C [auth E]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, C [auth E]	IPR004160	Translation elongation factor EFTu/EF1A, C-terminal	Domain
A, C [auth E]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D [auth F]	IPR004405	Translation release factor pelota	Family
B, D [auth F]	IPR005140	eRF1 domain 1/Pelota-like	Domain
B, D [auth F]	IPR042226	eRF1, domain 2 superfamily	Homologous Superfamily
B, D [auth F]	IPR038069	Pelota/DOM34, N-terminal domain	Homologous Superfamily
B, D [auth F]	IPR023521	Translation release factor pelota, archaea	Family
B, D [auth F]	IPR005142	eRF1 domain 3	Domain
B, D [auth F]	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily
E [auth X]	IPR022295	Large ribosomal subunit protein P1, archaea	Family
E [auth X]	IPR027534	Large ribosomal subunit protein P1/P2	Family
E [auth X]	IPR038716	Large ribosomal subunit protein P1/P2, N-terminal domain	Homologous Superfamily