2F1L | pdb_00002f1l

CRYSTAL STRUCTURE OF A PUTATIVE 16S RIBOSOMAL RNA PROCESSING PROTEIN RIMM (PA3744) FROM PSEUDOMONAS AERUGINOSA AT 2.46 A RESOLUTION

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)
A	d2f1la1	All beta proteins	PRC-barrel domain	PRC-barrel domain	RimM C-terminal domain-like	16S rRNA processing protein RimM, C-terminal domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
A	d2f1la2	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	RimM N-terminal domain-like	16S rRNA processing protein RimM, N-terminal domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	RimM C-terminal domain-like	8028081	4001810	SCOP2 (2022-06-29)
A	SCOP2 Family	RimM N-terminal domain-like	8028083	4001828	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PRC-barrel domain	8040460	3000637	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Translational proteins	8040462	3000811	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	RimM	e2f1lA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: RimM	ECOD (1.6)
A	PRC	e2f1lA2	A: beta barrels	X: SH3	H: PRC-barrel domain (From Topology)	T: PRC-barrel domain	F: PRC	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	PF24986	RimM PRC barrel domain (PRC_RimM)	RimM PRC barrel domain	This entry represents a PRC-barrel domain found in the RimM protein family. The RimM family comprises ribosome maturation factors essential for the final assembly of the 30S ribosomal subunit, particularly the head region. These proteins facilitate ...	This entry represents a PRC-barrel domain found in the RimM protein family. The RimM family comprises ribosome maturation factors essential for the final assembly of the 30S ribosomal subunit, particularly the head region. These proteins facilitate the efficient processing of 16S rRNA and may function both before and after RbfA during 16S rRNA maturation. RimM proteins have a specific affinity for free 30S ribosomal subunits but not for 70S ribosomes. The PRC barrel domain within these proteins binds to ribosomal protein uS19, playing a crucial role in the assembly process. In some organisms, RimM is one of several proteins, including Era, RbfA, and RsgA/YjeQ, that assist in the late stages of 30S subunit assembly, ensuring the correct assembly of head-associated ribosomal proteins and preventing the accumulation of precursor rRNA forms.	Domain
A	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	16S rRNA processing protein	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 ribosomal small subunit biogenesis nucleic acid metabolic process cellular component biogenesis nucleobase-containing compound metabolic process 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 ribosomal small subunit biogenesis nucleic acid metabolic process cellular component biogenesis nucleobase-containing compound metabolic process RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process maturation of SSU-rRNA cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process RNA processing rRNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle ribosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036976	RimM, N-terminal domain superfamily	Homologous Superfamily
A	IPR002676	RimM, N-terminal	Domain
A	IPR011961	Ribosome maturation factor RimM	Family
A	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A	IPR011033	PRC-barrel-like superfamily	Homologous Superfamily
A	IPR056792	Ribosome maturation factor RimM, 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.