3MOJ

Structure of the RNA binding domain of the Bacillus subtilis YxiN protein complexed with a fragment of 23S ribosomal RNA

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)
B	SCOP2B Superfamily	RNA-binding domain RBD	8054240	3000110	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)
B	DbpA	e3mojB1	A: a+b two layers	X: Alpha-beta plaits	H: RNA-binding domain, RBD (From Topology)	T: RNA-binding domain, RBD	F: DbpA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF03880	DbpA RNA binding domain (DbpA)	DbpA RNA binding domain	This RNA binding domain is found at the C-terminus of a number of DEAD helicase proteins [1]. It is sufficient to confer specificity for hairpin 92 of 23S rRNA, which is part of the ribosomal A-site. However, several members of this family lack spe ...	This RNA binding domain is found at the C-terminus of a number of DEAD helicase proteins [1]. It is sufficient to confer specificity for hairpin 92 of 23S rRNA, which is part of the ribosomal A-site. However, several members of this family lack specificity for 23S rRNA. These can proteins can generally be distinguished by a basic region that extends beyond this domain [Karl Kossen, unpublished data].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	RNA (69-MER)	-	-	-
B	ATP-dependent RNA helicase dbpA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA 3'-5' RNA helicase activity RNA strand annealing activity RNA binding annealing activity nucleic acid binding single-stranded RNA binding	response to stimulus response to stress response to abiotic stimulus response to cold response to temperature stimulus cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR001650	Helicase, C-terminal domain-like	Domain
B	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site	Conserved Site
B	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
B	IPR005580	DEAD box helicase DbpA/CsdA, RNA-binding domain	Domain
B	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
B	IPR028619	ATP-dependent RNA helicase DbpA	Family
B	IPR014014	RNA helicase, DEAD-box type, Q motif	Domain
B	IPR011545	DEAD/DEAH box helicase domain	Domain
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.