487D | pdb_0000487d

SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION

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)
C [auth J]	d487dj_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Large subunit	Prokaryotic (50S subunit)	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
D [auth K]	d487dk_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Large subunit	Prokaryotic (50S subunit)	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
F [auth M]	d487dm_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Large subunit	Prokaryotic (50S subunit)	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
G [auth N]	d487dn_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Large subunit	Prokaryotic (50S subunit)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E [auth L]	d487dl_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Large subunit	Prokaryotic (50S subunit)	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B [auth I]	d487di_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Large subunit	Prokaryotic (50S subunit)	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
A [auth H]	d487dh_	Low resolution protein structures	Ribosome and ribosomal fragments	Ribosome and ribosomal fragments	Large subunit	Prokaryotic (50S subunit)	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth J]	SCOP2B Superfamily	Ribosomal protein L6	8036508	3000724	SCOP2B (2022-06-29)
C [auth J]	SCOP2B Superfamily	Ribosomal protein L6	8036504	3000724	SCOP2B (2022-06-29)
D [auth K]	SCOP2B Superfamily	Ribosomal protein L9 C-domain	8035874	3000329	SCOP2B (2022-06-29)
D [auth K]	SCOP2B Superfamily	L9 N-domain-like	8042225	3000338	SCOP2B (2022-06-29)
F [auth M]	SCOP2B Superfamily	50S Ribosomal protein L14-like	8041752	3000433	SCOP2B (2022-06-29)
G [auth N]	SCOP2B Superfamily	Ribosomal protein L25-like	8042538	3001161	SCOP2B (2022-06-29)
E [auth L]	SCOP2B Superfamily	Ribosomal L11/L12e N-terminal domain-like	8035082	3000950	SCOP2B (2022-06-29)
E [auth L]	SCOP2B Superfamily	Ribosomal protein L11, C-terminal domain	8036651	3001186	SCOP2B (2022-06-29)
B [auth I]	SCOP2B Superfamily	Nucleic acid-binding proteins	8041953	3000135	SCOP2B (2022-06-29)
B [auth I]	SCOP2B Superfamily	Translation proteins SH3-like KOW motif containing domain	8041672	3000334	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)
C [auth J]	Flavi_glycoprot	e487dJ1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Flavi_glycoprot	ECOD (v294.1)
D [auth K]	Flavi_glycoprot	e487dK1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Flavi_glycoprot	ECOD (v294.1)
F [auth M]	Flavi_glycoprot	e487dM1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Flavi_glycoprot	ECOD (v294.1)
G [auth N]	Flavi_glycoprot	e487dN1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Flavi_glycoprot	ECOD (v294.1)
E [auth L]	Flavi_glycoprot	e487dL1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Flavi_glycoprot	ECOD (v294.1)
B [auth I]	Flavi_glycoprot	e487dI1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Flavi_glycoprot	ECOD (v294.1)
A [auth H]	Flavi_glycoprot	e487dH1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: Flavi_glycoprot	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth N]	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
E [auth L]	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
E [auth L]	PF00298	Ribosomal protein L11, RNA binding domain (Ribosomal_L11)	Ribosomal protein L11, RNA binding domain		Domain
A [auth H]	PF00687	Ribosomal protein L1p/L10e family (Ribosomal_L1)	Ribosomal protein L1p/L10e family	This family includes prokaryotic L1 and eukaryotic L10.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth J]	50S ribosomal protein L6	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic 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
D [auth K]	50S ribosomal protein L9	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 ribonucleoprotein complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle ribosome
F [auth M]	50S ribosomal protein L14	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding large ribosomal subunit 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
G [auth N]	50S ribosomal protein L25	RNA binding binding rRNA binding 5S rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process cytoplasmic translation response to stimulus response to radiation response to abiotic stimulus ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal large subunit biogenesis protein-RNA complex assembly cellular component biogenesis cellular component organization ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly ribosomal large subunit assembly protein-containing complex assembly cellular component organization or biogenesis 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
E [auth L]	50S ribosomal protein L11	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding large ribosomal subunit 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 I]	50S ribosomal protein L2	RNA binding binding rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome transferase activity catalytic activity	primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome large ribosomal subunit
A [auth H]	50S ribosomal protein L1	RNA binding binding tRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome rRNA binding	regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process regulation of metabolic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome large ribosomal subunit

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth J]	IPR020040	Large ribosomal subunit protein uL6, alpha-beta domain	Domain
C [auth J]	IPR036789	Large ribosomal subunit protein uL6-like, alpha-beta domain superfamily	Homologous Superfamily
C [auth J]	IPR000702	Large ribosomal subunit protein uL6-like	Family
C [auth J]	IPR019906	Large ribosomal subunit protein uL6, bacteria	Family
C [auth J]	IPR002358	Large ribosomal subunit protein uL6, conserved site	Conserved Site
D [auth K]	IPR009027	Large ribosomal subunit protein bL9/RNase H1, N-terminal	Homologous Superfamily
D [auth K]	IPR020594	Large ribosomal subunit protein bL9, bacteria/chloroplast	Family
D [auth K]	IPR036935	Large ribosomal subunit protein bL9, N-terminal domain superfamily	Homologous Superfamily
D [auth K]	IPR036791	Large ribosomal subunit protein bL9, C-terminal domain superfamily	Homologous Superfamily
D [auth K]	IPR020069	Large ribosomal subunit protein bL9, C-terminal	Domain
D [auth K]	IPR020070	Large ribosomal subunit protein bL9, N-terminal	Domain
D [auth K]	IPR000244	Large ribosomal subunit protein bL9	Family
F [auth M]	IPR036853	Large ribosomal subunit protein uL14 superfamily	Homologous Superfamily
F [auth M]	IPR000218	Large ribosomal subunit protein uL14	Family
F [auth M]	IPR019972	Large ribosomal subunit protein uL14, conserved site	Conserved Site
F [auth M]	IPR005745	Large ribosomal subunit protein uL14, bacteria	Family
G [auth N]	IPR020055	Ribosomal protein bL25, short-form	Family
G [auth N]	IPR029751	Large ribosomal subunit protein bL25, L25 domain	Domain
G [auth N]	IPR020056	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, N-terminal	Homologous Superfamily
G [auth N]	IPR011035	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, anti-codon-binding domain superfamily	Homologous Superfamily
G [auth N]	IPR020930	Large ribosomal subunit protein uL5, bacteria	Family
E [auth L]	IPR020785	Large ribosomal subunit protein uL11, conserved site	Conserved Site
E [auth L]	IPR020783	Large ribosomal subunit protein uL11, C-terminal	Domain
E [auth L]	IPR000911	Ribosomal protein uL11	Family
E [auth L]	IPR036769	Large ribosomal subunit protein uL11, C-terminal domain superfamily	Homologous Superfamily
E [auth L]	IPR020784	Large ribosomal subunit protein uL11, N-terminal	Domain
E [auth L]	IPR036796	Large ribosomal subunit protein uL11, N-terminal domain superfamily	Homologous Superfamily
E [auth L]	IPR006519	Large ribosomal subunit protein uL11, bacteria	Family
B [auth I]	IPR005880	Large ribosomal subunit protein uL2, bacteria/organella	Family
B [auth I]	IPR022669	Large ribosomal subunit protein uL2, C-terminal	Domain
B [auth I]	IPR014722	Large ribosomal subunit protein uL2, domain 2	Homologous Superfamily
B [auth I]	IPR008991	Translation protein SH3-like domain superfamily	Homologous Superfamily
B [auth I]	IPR022671	Large ribosomal subunit protein uL2, conserved site	Conserved Site
B [auth I]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
B [auth I]	IPR022666	Large ribosomal subunit protein uL2, RNA-binding domain	Domain
B [auth I]	IPR014726	Large ribosomal subunit protein uL2, domain 3	Homologous Superfamily
B [auth I]	IPR002171	Large ribosomal subunit protein uL2	Family
A [auth H]	IPR023673	Large ribosomal subunit protein uL1, conserved site	Conserved Site
A [auth H]	IPR005878	Large ribosomal subunit protein uL1, bacteria	Family
A [auth H]	IPR016095	Large ribosomal subunit protein uL1, 3-layer alpha/beta-sandwich domain	Homologous Superfamily
A [auth H]	IPR023674	Ribosomal protein uL1-like	Homologous Superfamily
A [auth H]	IPR002143	Large ribosomal subunit protein uL1	Family
A [auth H]	IPR028364	Ribosomal protein uL1/ribosomal biogenesis protein	Family