1IB8 | pdb_00001ib8

SOLUTION STRUCTURE AND FUNCTION OF A CONSERVED PROTEIN SP14.3 ENCODED BY AN ESSENTIAL STREPTOCOCCUS PNEUMONIAE GENE

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	d1ib8a1	All beta proteins	Sm-like fold	YhbC-like, C-terminal domain	YhbC-like, C-terminal domain	Hypothetical protein SP14.3 (SP0552)	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)
A	d1ib8a2	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	YhbC-like, N-terminal domain	YhbC-like, N-terminal domain	Hypothetical protein SP14.3 (SP0552)	(Streptococcus pneumoniae ) [TaxId: 1313 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	YhbC-like, C-terminal domain	8027175	4002169	SCOP2 (2022-06-29)
A	SCOP2 Family	YhbC-like, N-terminal domain	8027176	4002612	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YhbC-like, C-terminal domain	8039554	3000906	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	YhbC-like, N-terminal domain	8039555	3001482	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	DUF150_C	e1ib8A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: DUF150_C	ECOD (v294.2)
A	RimP_N	e1ib8A2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: YhbC-like, N-terminal domain	T: YhbC-like, N-terminal domain	F: RimP_N	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.300.70	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
A	2.30.30.180	Mainly Beta	Roll	SH3 type barrels.	Ribosome maturation factor RimP, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF17384	RimP C-terminal Sm-like domain (RimP_C)	RimP C-terminal Sm-like domain	This family represents the C-terminal domain from the bacterial ribosome assembly factor RimP. In Gram-negative bacteria, RimP knockout causes slow cell growth whereas in Gram-positive Streptococcus pneumoniae, the deletion of RimP is lethal. RimP is ...	This family represents the C-terminal domain from the bacterial ribosome assembly factor RimP. In Gram-negative bacteria, RimP knockout causes slow cell growth whereas in Gram-positive Streptococcus pneumoniae, the deletion of RimP is lethal. RimP is essential for survival under stress conditions in Mycobacterium. RimP is seen in four ribosome assembly states (states A to D) bound on the front of the 30S subunit [2]. RimP contains two domains, an N-terminal and a C-terminal domain having a Sm-like fold, characteristic of the Sm/Lsm superfamily proteins, connected by an unstructured region [1,2].	Domain
A	PF02576	RimP N-terminal domain (RimP_N)	RimP N-terminal domain	This entry represents the N-terminal domain of the ribosome maturation factor RimP (also known as yhbC). RimP facilitates the maturation of the 30S ribosomal subunit [1]. The N-terminal domain contains two alpha-helices and a three-stranded beta-shee ...	This entry represents the N-terminal domain of the ribosome maturation factor RimP (also known as yhbC). RimP facilitates the maturation of the 30S ribosomal subunit [1]. The N-terminal domain contains two alpha-helices and a three-stranded beta-sheet. It is suggested that the N-terminal domain of SP14.3 (RimP orthologue) could function as a protein module that binds to other proteins, especially those that contain highly positively charged surfaces. [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CONSERVED PROTEIN SP14.3	-	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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR028989	Ribosome maturation factor RimP, N-terminal	Domain
A	IPR003728	Ribosome maturation factor RimP	Family
A	IPR036847	Ribosome maturation factor RimP, C-terminal domain superfamily	Homologous Superfamily
A	IPR035956	RimP, N-terminal domain superfamily	Homologous Superfamily
A	IPR028998	Ribosome maturation factor RimP, C-terminal	Domain

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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.