1NJM | pdb_00001njm

The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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 T]	d1njmt_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Large subunit	Prokaryotic (50S subunit)	(Deinococcus radiodurans ) [TaxId: 1299 ],	SCOPe (2.08)
C [auth K]	d1njmk_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Large subunit	Prokaryotic (50S subunit)	(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)
D [auth T]	SCOP2B Superfamily	Ribosomal protein L25-like	8038580	3001161	SCOP2B (2022-06-29)
C [auth K]	SCOP2B Superfamily	Ribosomal protein L16p/L10e	8038562	3000884	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)
D [auth T]	PF25869	e1njmT1	A: a/b three-layered sandwiches	X: Single-stranded left-handed beta-helix	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF25869	ECOD (v294.1)
C [auth K]	AP_endonuc_2	e1njmK1	A: a/b three-layered sandwiches	X: Cytochrome P450	H: Cytochrome P450	T: Cytochrome P450	F: AP_endonuc_2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth T]	PF14693	Ribosomal protein TL5, C-terminal domain (Ribosomal_TL5_C)	Ribosomal protein TL5, C-terminal domain	This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, Pfam:PF01386. Full length (N- and C-terminal domain) homologues of TL5 are also known as CTC pr ...	This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, Pfam:PF01386. Full length (N- and C-terminal domain) homologues of TL5 are also known as CTC proteins. TL5 or CTC are not found in Eukarya or Archaea. In some Bacteria, including E. coli, this ribosomal subunit occurs as a single domain protein (named Ribosomal subunit L25), where the only domain is homologous to TL5 N-terminal domain (hence included in family Pfam:PF01386). The function of the C-terminal domain of TLC is at present unknown.	Domain
D [auth T]	PF01386	Ribosomal L25p family (Ribosomal_L25p)	Ribosomal L25p family	Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis Swiss:P14194, which is induced by stress.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth T]	GENERAL STRESS PROTEIN CTC	RNA binding binding rRNA binding 5S rRNA binding nucleic acid binding tRNA binding structural molecule activity structural constituent of ribosome	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 K]	50S ribosomal protein L16	RNA binding binding tRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome rRNA 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 5]	tRNA acceptor stem mimic	-	-	-
A [auth 0]	23S ribosomal RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth T]	IPR011035	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, anti-codon-binding domain superfamily	Homologous Superfamily
D [auth T]	IPR001021	Ribosomal protein bL25, long-form	Family
D [auth T]	IPR029751	Large ribosomal subunit protein bL25, L25 domain	Domain
D [auth T]	IPR037121	Large ribosomal subunit protein bL25, C-terminal	Homologous Superfamily
D [auth T]	IPR020057	Large ribosomal subunit protein bL25, beta domain	Domain
D [auth T]	IPR020056	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, N-terminal	Homologous Superfamily
D [auth T]	IPR020930	Large ribosomal subunit protein uL5, bacteria	Family
C [auth K]	IPR000114	Large ribosomal subunit protein uL16, bacteria	Family
C [auth K]	IPR036920	Large ribosomal subunit protein uL16 superfamily	Homologous Superfamily
C [auth K]	IPR020798	Large ribosomal subunit protein uL16, conserved site	Conserved Site
C [auth K]	IPR016180	Large ribosomal subunit protein uL16 domain	Domain
C [auth K]	IPR047873	Large ribosomal subunit protein uL16	Family

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.