2D3O | pdb_00002d3o

Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth W]	d2d3ow1	All alpha proteins	Long alpha-hairpin	Ribosomal protein L29 (L29p)	Ribosomal protein L29 (L29p)	Ribosomal protein L29 (L29p)	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
C [auth S]	d2d3os1	All beta proteins	SH3-like barrel	Translation proteins SH3-like domain	Ribosomal proteins L24p and L21e	Ribosomal proteins L24 (L24p)	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
B [auth R]	d2d3or1	Alpha and beta proteins (a+b)	Ribosomal proteins S24e, L23 and L15e	Ribosomal proteins S24e, L23 and L15e	L23p	Ribosomal protein L23	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth 1]	SCOP2B Superfamily	Trigger factor ribosome-binding domain	8075114	3001141	SCOP2B (2022-06-29)
D [auth W]	SCOP2B Superfamily	Ribosomal protein L29 (L29p)	8038586	3000713	SCOP2B (2022-06-29)
C [auth S]	SCOP2B Superfamily	Translation proteins SH3-like KOW motif containing domain	8038578	3000334	SCOP2B (2022-06-29)
B [auth R]	SCOP2B Superfamily	Ribosomal proteins S24e, L23 and L15e	8038577	3000210	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)
E [auth 1]	Trigger_N	e2d3o13	A: a+b two layers	X: Glucose permease domain IIB-like	H: Trigger factor ribosome-binding domain (From Topology)	T: Trigger factor ribosome-binding domain	F: Trigger_N	ECOD (1.6)
D [auth W]	Ribosomal_L29	e2d3oW1	A: alpha bundles	X: Long alpha-hairpin	H: Ribosomal protein L29 (L29p) (From Topology)	T: Ribosomal protein L29 (L29p)	F: Ribosomal_L29	ECOD (1.6)
C [auth S]	ribosomal_L24_1	e2d3oS2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: ribosomal_L24_1	ECOD (1.6)
B [auth R]	Ribosomal_L23_2	e2d3oR1	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal proteins S24e, L23 and L15e (From Topology)	T: Ribosomal proteins S24e, L23 and L15e	F: Ribosomal_L23_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth 1]	3.30.70.1050	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Trigger factor ribosome-binding domain	CATH (4.3.0)
D [auth W]	1.10.287.310	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B [auth R]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth W]	PF00831	Ribosomal L29 protein (Ribosomal_L29)	Ribosomal L29 protein	-	Family
C [auth S]	PF17136	Large ribosomal subunit protein uL24, C-terminal domain (ribosomal_L24)	Large ribosomal subunit protein uL24, C-terminal domain	This entry describes the C-terminal domain in large ribosomal subunit protein uL24 (also known as RPL26). RPL26 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. RPL26 m ...	This entry describes the C-terminal domain in large ribosomal subunit protein uL24 (also known as RPL26). RPL26 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. RPL26 makes very minor contributions to the biogenesis structure, and function of 60s ribosomal subunits [1]. However, RPL24 is essential to generate the first intermediate during 50s ribosomal subunits assembly [2]. RPL26 have an extra-ribosomal function to enhances p53 translation after DNA damage [3].	Domain
C [auth S]	PF00467	KOW motif (KOW)	KOW motif	-	Family
B [auth R]	PF00276	Ribosomal protein L23 (Ribosomal_L23)	Ribosomal protein L23	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth 1]	Trigger Factor	isomerase activity catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity RNA binding binding rRNA binding nucleic acid binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding protein folding chaperone	primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process 'de novo' cotranslational protein folding metabolic process cellular process protein metabolic process macromolecule metabolic process 'de novo' protein folding protein unfolding cell division primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein folding biosynthetic process 'de novo' cotranslational protein folding metabolic process cellular process protein metabolic process macromolecule metabolic process 'de novo' protein folding protein unfolding cell division localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization	cellular anatomical structure intracellular anatomical structure cytoplasm
D [auth W]	50S RIBOSOMAL PROTEIN L29	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol large ribosomal subunit
C [auth S]	50S RIBOSOMAL PROTEIN L24	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol large ribosomal subunit
B [auth R]	50S RIBOSOMAL PROTEIN L23	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol large ribosomal subunit
A [auth 0]	23S RIBOSOMAL RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth 1]	IPR046357	Peptidyl-prolyl cis-trans isomerase domain superfamily	Homologous Superfamily
E [auth 1]	IPR036611	Trigger factor ribosome-binding domain superfamily	Homologous Superfamily
E [auth 1]	IPR008881	Trigger factor, ribosome-binding, bacterial	Domain
E [auth 1]	IPR027304	Trigger factor/SurA domain superfamily	Homologous Superfamily
E [auth 1]	IPR037041	Trigger factor, C-terminal domain superfamily	Homologous Superfamily
E [auth 1]	IPR008880	Trigger factor, C-terminal	Domain
E [auth 1]	IPR005215	Trigger factor	Family
D [auth W]	IPR050063	Universal ribosomal protein uL29	Family
D [auth W]	IPR001854	Large ribosomal subunit protein uL29	Family
D [auth W]	IPR036049	Large ribosomal subunit protein uL29 superfamily	Homologous Superfamily
D [auth W]	IPR018254	Large ribosomal subunit protein uL29, conserved site	Conserved Site
C [auth S]	IPR003256	Large ribosomal subunit protein uL24	Family
C [auth S]	IPR041988	Large ribosomal subunit protein uL24, KOW domain	Domain
C [auth S]	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
C [auth S]	IPR005824	KOW	Domain
C [auth S]	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
C [auth S]	IPR005825	Large ribosomal subunit protein uL24, conserved site	Conserved Site
B [auth R]	IPR012678	Ribosomal protein uL23/eL15/eS24 core domain superfamily	Homologous Superfamily
B [auth R]	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
B [auth R]	IPR001014	Large ribosomal subunit protein uL23, conserved site	Conserved Site
B [auth R]	IPR013025	Large ribosomal subunit protein uL23-like	Family