3OBY | pdb_00003oby

Crystal structure of Archaeoglobus fulgidus Pelota reveals inter-domain structural plasticity

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	eRF1_1	e3obyB1	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	e3obyB3	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	e3obyB2	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)
A	eRF1_1	e3obyA1	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	eRF1_3	e3obyA2	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	eRF1_2	e3obyA3	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)
B	2.30.30.870	Mainly Beta	Roll	SH3 type barrels.	Pelota, domain A	CATH (4.3.0)
B	3.30.420.60	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)
A	2.30.30.870	Mainly Beta	Roll	SH3 type barrels.	Pelota, domain A	CATH (4.3.0)
A	3.30.420.60	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.30.1330.30	Alpha Beta	2-Layer Sandwich	60s Ribosomal Protein L30	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
A, B	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, B	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, B	IPR004405	Pelota	Family
A, B	IPR005141	eRF1 domain 2	Domain
A, B	IPR042226	eRF1, domain 2 superfamily	Homologous Superfamily
A, B	IPR023521	Pelota, archaea	Family
A, B	IPR038069	Pelota/DOM34, N-terminal domain	Homologous Superfamily
A, B	IPR058547	Pelota, N-terminal domain	Domain
A, B	IPR005142	eRF1 domain 3	Domain
A, B	IPR005140	eRF1/Pelota-like, N-terminal domain	Domain
A, B	IPR029064	Ribosomal protein eL30-like superfamily	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.