3J0D | pdb_00003j0d

Models for the T. thermophilus ribosome recycling factor bound to the E. coli post-termination complex

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)
J [auth I]	SCOP2 Family	Cold shock DNA-binding domain-like	8106544	4001909	SCOP2 (2022-06-29)
J [auth I]	SCOP2 Superfamily	Nucleic acid-binding proteins	8106545	3000135	SCOP2 (2022-06-29)
K [auth J]	SCOP2B Superfamily	Ribosome recycling factor, RRF	8035749	3001524	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribosomal L11/L12e N-terminal domain-like	8032963	3000950	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribosomal protein L11, C-terminal domain	8032961	3001186	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)
J [auth I]	Ribosom_S12_S23	e3j0dI1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Ribosom_S12_S23	ECOD (1.6)
K [auth J]	RRF	e3j0dJ1	A: a+b two layers	X: RRF/tRNA synthetase additional domain-like	H: Ribosome recycling factor, RRF (From Topology)	T: Ribosome recycling factor, RRF	F: RRF	ECOD (1.6)
G	Ribosomal_L11	e3j0dG1	A: alpha arrays	X: HTH	H: HTH	T: Ribosomal protein L11, C-terminal domain	F: Ribosomal_L11	ECOD (1.6)
G	Ribosomal_L11_N	e3j0dG2	A: a+b two layers	X: Ribosomal protein L11/L12e N-terminal domain-like	H: Ribosomal protein L11/L12e N-terminal domain (From Topology)	T: Ribosomal protein L11/L12e N-terminal domain	F: Ribosomal_L11_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
J [auth I]	PF00164	Ribosomal protein S12/S23 (Ribosom_S12_S23)	Ribosomal protein S12/S23	This protein is known as S12 in bacteria and archaea and S23 in eukaryotes.	Domain
K [auth J]	PF01765	Ribosome recycling factor (RRF)	Ribosome recycling factor	The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth [1]. Thus ribosomes are "recycled" and ready for another round of protein synthe ...	The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth [1]. Thus ribosomes are "recycled" and ready for another round of protein synthesis.	Domain
G	PF03946	Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N)	Ribosomal protein L11, N-terminal domain	The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain.	Domain
G	PF00298	Ribosomal protein L11, RNA binding domain (Ribosomal_L11)	Ribosomal protein L11, RNA binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ribosomal 23S RNA	-	-	-
J [auth I]	30S ribosomal protein S12	RNA binding binding rRNA binding nucleic acid binding misfolded RNA binding tRNA binding structural molecule activity structural constituent of ribosome	regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process RNA processing positive regulation of cellular process regulation of biosynthetic process regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process RNA processing positive regulation of cellular process regulation of biosynthetic process RNA splicing regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of RNA splicing macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process positive regulation of gene expression metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of RNA splicing regulation of metabolic process cytoplasmic translation protein metabolic process translation RNA folding Group I intron splicing RNA splicing, via transesterification reactions with guanosine as nucleophile RNA splicing, via transesterification reactions response to stimulus response to chemical response to antibiotic maintenance of translational fidelity	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex small ribosomal subunit intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome
K [auth J]	Ribosome-recycling factor	ribonucleoprotein complex binding protein-containing complex binding binding ribosomal large subunit binding ribosome binding	cellular component disassembly protein-containing complex organization protein-containing complex disassembly primary metabolic process translation gene expression macromolecule biosynthetic process cellular component organization biosynthetic process cellular process metabolic process translational termination cellular component organization or biogenesis protein metabolic process cellular component disassembly protein-containing complex organization protein-containing complex disassembly primary metabolic process translation gene expression macromolecule biosynthetic process cellular component organization biosynthetic process cellular process metabolic process translational termination cellular component organization or biogenesis protein metabolic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
B	ribosomal 23S RNA	-	-	-
C	ribosomal 23S RNA	-	-	-
D	ribosomal 23S RNA	-	-	-
E	ribosomal 23S RNA	-	-	-
F	ribosomal 23S RNA	-	-	-
G	50S ribosomal protein L11	RNA binding binding rRNA binding nucleic acid binding large ribosomal subunit rRNA binding structural molecule activity structural constituent of ribosome	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress stringent response cellular process response to starvation cellular response to starvation biosynthetic process cytoplasmic translation metabolic process primary metabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress stringent response cellular process response to starvation cellular response to starvation biosynthetic process cytoplasmic translation metabolic process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process cellular component disassembly protein-containing complex organization protein-containing complex disassembly cellular component organization translational termination cellular component organization or biogenesis ribonucleoprotein complex biogenesis organelle assembly membraneless organelle assembly ribosomal large subunit biogenesis protein-RNA complex assembly cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly ribosomal large subunit assembly protein-containing complex assembly ribosome assembly	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome large ribosomal subunit
H	ribosomal 16S RNA	-	-	-
I [auth h]	ribosomal 16S RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
J [auth I]	IPR005679	Ribosomal protein uS12, bacterial-type	Family
J [auth I]	IPR006032	Small ribosomal subunit protein uS12	Family
J [auth I]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
K [auth J]	IPR023584	Ribosome recycling factor domain	Domain
K [auth J]	IPR036191	RRF superfamily	Homologous Superfamily
K [auth J]	IPR002661	Ribosome recycling factor	Family
G	IPR020785	Large ribosomal subunit protein uL11, conserved site	Conserved Site
G	IPR020783	Large ribosomal subunit protein uL11, C-terminal	Domain
G	IPR000911	Ribosomal protein uL11	Family
G	IPR006519	Large ribosomal subunit protein uL11, bacterial-type	Family
G	IPR020784	Large ribosomal subunit protein uL11, N-terminal	Domain
G	IPR036769	Large ribosomal subunit protein uL11, C-terminal domain superfamily	Homologous Superfamily
G	IPR036796	Large ribosomal subunit protein uL11, N-terminal domain 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.