6JI2 | pdb_00006ji2

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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth E]	e6ji2E1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: SBP_bac_6	F:	ECOD (20:10:01)
A	e6ji2A1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: SBP_bac_6	F:	ECOD (20:10:01)
D [auth F]	e6ji2F1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: SBP_bac_6	F:	ECOD (20:10:01)
B	e6ji2B1	A: Nat/Ivy	X: Acyl-CoA N-acyltransferases (Nat)	H: Acyl-CoA N-acyltransferases (Nat)	T: SBP_bac_6	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)

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]	PF26356	Pelota N-terminal domain (Pelota_N)	Pelota N-terminal domain	This entry represents the N-terminal domain found in Pelota family proteins. The Pelota protein family is involved in recognizing stalled ribosomes and facilitating the No-Go Decay (NGD) pathway. Members of this family can destabilize mRNA in the rib ...	This entry represents the N-terminal domain found in Pelota family proteins. The Pelota protein family is involved in recognizing stalled ribosomes and facilitating the No-Go Decay (NGD) pathway. Members of this family can destabilize mRNA in the ribosome channel, promoting the disassembly of stalled ribosomes and subsequent degradation of damaged mRNAs. In eukaryotes, the Pelota-HBS1L complex, which includes Pelota proteins, plays a critical role in these processes. Additionally, Pelota proteins are implicated in mitochondrial quality control through mitophagy, where they are recruited to damaged mitochondria to facilitate the recruitment of autophagy receptors. The family is characterized by an RNA-binding Sm fold domain that harbors endoribonuclease activity, essential for its function in mRNA cleavage and ribosome rescue.	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

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	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding translation factor activity translation elongation factor activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding translation factor activity translation elongation 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 anatomical structure intracellular anatomical structure cytoplasm
E [auth X]	Archaeal ribosomal stalk protein aP1	structural molecule activity structural constituent of ribosome	primary metabolic process translation gene expression macromolecule biosynthetic process protein biosynthetic process biosynthetic process translational elongation metabolic process cellular process macromolecule metabolic process protein metabolic process	protein-containing complex ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome
B, D [auth F]	Protein pelota homolog	hydrolase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid cation binding ion binding binding metal ion binding small molecule binding	regulation of cellular 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 regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular 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 regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation nuclear-transcribed mRNA catabolic process, non-stop decay primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic 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	cellular anatomical structure intracellular anatomical structure cytoplasm

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]	IPR054696	GTP-eEF1A, C-terminal domain	Domain
A, C [auth E]	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, C [auth E]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
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
E [auth X]	IPR022295	Large ribosomal subunit protein P1, archaeal	Family
B, D [auth F]	IPR004405	Pelota	Family
B, D [auth F]	IPR042226	eRF1, domain 2 superfamily	Homologous Superfamily
B, D [auth F]	IPR023521	Pelota, archaea	Family
B, D [auth F]	IPR038069	Pelota/DOM34, N-terminal domain	Homologous Superfamily
B, D [auth F]	IPR058547	Pelota, N-terminal domain	Domain
B, D [auth F]	IPR005142	eRF1 domain 3	Domain
B, D [auth F]	IPR005140	eRF1/Pelota-like, N-terminal domain	Domain
B, D [auth F]	IPR029064	Ribosomal protein eL30-like superfamily	Homologous Superfamily