3A1P | pdb_00003a1p

Structure of Ribosome maturation protein RimM and Ribosomal protein S19

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ribosomal protein S19	8044027	3000686	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S19	8044027	3000686	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	Ribosomal_S19	e3a1pD1	A: alpha bundles	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: Ribosomal_S19	ECOD (develop294)
B	Ribosomal_S19	e3a1pB1	A: alpha bundles	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: Ribosomal_S19	ECOD (develop294)
C	RVP	e3a1pC1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (develop294)
A	PA-IL	e3a1pA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Galactose-binding domain-like	T: Galactose-binding domain-like	F: PA-IL	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.860.10	Alpha Beta	2-Layer Sandwich	30s Ribosomal Protein S19	Chain A	CATH (4.3.0)
B	3.30.860.10	Alpha Beta	2-Layer Sandwich	30s Ribosomal Protein S19	Chain A	CATH (4.3.0)
C	2.40.30.60	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C	2.30.30.240	Mainly Beta	Roll	SH3 type barrels.	PRC-barrel domain	CATH (4.3.0)
A	2.40.30.60	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	2.30.30.240	Mainly Beta	Roll	SH3 type barrels.	PRC-barrel domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF01782	RimM N-terminal domain (RimM)	RimM N-terminal domain	The RimM protein is essential for efficient processing of 16S rRNA [1]. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes [1]. This N-terminal domain is found associated with a ...	The RimM protein is essential for efficient processing of 16S rRNA [1]. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes [1]. This N-terminal domain is found associated with a PRC-barrel domain [2].	Domain
A, C	PF05239	PRC-barrel domain (PRC)	PRC-barrel domain	The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, ...	The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the carboxyl terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	30S ribosomal protein S19	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding	ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis ribosome assembly biosynthetic process metabolic 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 small ribosomal subunit intracellular membraneless organelle ribosomal subunit intracellular organelle cellular anatomical structure ribonucleoprotein complex organelle membraneless organelle ribosome cytoplasm
A, C	Ribosome maturation factor rimM	ribonucleoprotein complex binding protein-containing complex binding binding ribosome binding	ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process ribonucleoprotein complex biogenesis RNA metabolic process primary metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process ribosomal small subunit biogenesis	cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle organelle membraneless organelle intracellular membraneless organelle ribosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR005732	Small ribosomal subunit protein uS19, bacteria	Family
B, D	IPR002222	Small ribosomal subunit protein uS19	Family
B, D	IPR023575	Small ribosomal subunit protein uS19, superfamily	Homologous Superfamily
B, D	IPR020934	Small ribosomal subunit protein uS19, conserved site	Conserved Site
A, C	IPR036976	RimM, N-terminal domain superfamily	Homologous Superfamily
A, C	IPR002676	RimM, N-terminal	Domain
A, C	IPR011961	Ribosome maturation factor RimM	Family
A, C	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, C	IPR011033	PRC-barrel-like superfamily	Homologous Superfamily
A, C	IPR027275	PRC-barrel domain	Domain

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.