7PMQ

DEAD-box helicase DbpA in the active conformation bound to a hairpin loop RNA and ADP/BeF3

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth C]	DbpA	e7pmqC3	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)
A [auth C]	DEAD	e7pmqC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD	ECOD (1.6)
A [auth C]	Helicase_C	e7pmqC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C	ECOD (1.6)
B [auth A]	DbpA	e7pmqA3	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)
B [auth A]	DEAD	e7pmqA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD	ECOD (1.6)
B [auth A]	Helicase_C	e7pmqA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C	ECOD (1.6)
C [auth B]	DbpA	e7pmqB3	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)
C [auth B]	DEAD	e7pmqB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD	ECOD (1.6)
C [auth B]	Helicase_C	e7pmqB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C	ECOD (1.6)
D	DbpA	e7pmqD3	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)
D	DEAD	e7pmqD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: DEAD	ECOD (1.6)
D	Helicase_C	e7pmqD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth C]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A [auth C]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (utative)
B [auth A]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
B [auth A]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (utative)
C [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
C [auth B]	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (utative)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
D	3.30.70.330	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	RRM (RNA recognition motif) domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth A], C [auth B], D	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
A [auth C], B [auth A], C [auth B], D	PF00270	DEAD/DEAH box helicase (DEAD)	DEAD/DEAH box helicase	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome ...	Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.	Domain
A [auth C], B [auth A], C [auth B], D	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth A], C [auth B], D	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 anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA DNA translocase activity catalytic activity, acting on a nucleic acid chromatin extrusion motor activity catalytic activity ATP-dependent activity ADP binding ATP-dependent H3-H4 histone complex chaperone activity catalytic activity, acting on a protein histone chaperone activity ATP-dependent chromatin remodeler activity H3-H4 histone complex chaperone activity protein carrier chaperone ATP-dependent histone chaperone activity molecular carrier activity cohesin loader activity DNA clamp loader activity DNA/RNA helicase activity catalytic activity, acting on RNA helicase activity ATP-dependent activity, acting on RNA RNA binding rRNA binding nucleic acid 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 ATP-dependent H2AZ histone chaperone activity RNA helicase activity 3'-5' RNA helicase activity	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 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 process cellular component organization or biogenesis ribosome assembly	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
E, F, G, H	RNA (42-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth A], C [auth B], D	IPR001650	Helicase, C-terminal domain-like	Domain
A [auth C], B [auth A], C [auth B], D	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site	Conserved Site
A [auth C], B [auth A], C [auth B], D	IPR050079	DEAD box RNA helicase	Family
A [auth C], B [auth A], C [auth B], D	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A [auth C], B [auth A], C [auth B], D	IPR005580	DEAD box helicase DbpA/CsdA, RNA-binding domain	Domain
A [auth C], B [auth A], C [auth B], D	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A [auth C], B [auth A], C [auth B], D	IPR028619	ATP-dependent RNA helicase DbpA	Family
A [auth C], B [auth A], C [auth B], D	IPR011545	DEAD/DEAH box helicase domain	Domain
A [auth C], B [auth A], C [auth B], D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.