4PJ3 | pdb_00004pj3

Structural insight into the function and evolution of the spliceosomal helicase Aquarius, Structure of Aquarius in complex with AMPPNP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4pj3a2	All alpha proteins	alpha-alpha superhelix	ARM repeat	Pre-mRNA splicing factor Cwf11 N-terminal domain-like	Pre-mRNA splicing factor Cwf11 / Aquarius	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4pj3a1	All beta proteins	Domain of alpha and beta subunits of F1 ATP synthase-like	Upf1 barrel domain-like	Upf1 barrel domain-like	Pre-mRNA splicing factor Cwf11 / Aquarius barrel domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4pj3a4	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Pre-mRNA splicing factor Cwf11 / Aquarius, C-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4pj3a3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Pre-mRNA splicing factor Cwf11 / Aquarius, N-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Aquarius N-terminal domain-like	8045528	4004517	SCOP2 (2022-06-29)
A	SCOP2 Family	Aquarius beta-barrel domain-like	8048214	4007716	SCOP2 (2022-06-29)
A	SCOP2 Family	Tandem AAA-ATPase domain	8048221	4000282	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ARM repeat-like	8090869	3000116	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Upf1 beta-barrel domain-like	8090870	3002168	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8090871	3002019	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8090872	3002019	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	Aquarius_N_2nd	e4pj3A2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Aquarius_N_2nd	ECOD (1.6)
A	Aquarius_N_1st	e4pj3A1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Aquarius_N_1st	ECOD (1.6)
A	Aquarius_N_3rd	e4pj3A5	A: a+b two layers	X: Spliceosomal helicase Aquarius insert domain (From Topology)	H: Spliceosomal helicase Aquarius insert domain (From Topology)	T: Spliceosomal helicase Aquarius insert domain	F: Aquarius_N_3rd	ECOD (1.6)
A	AAA_11_1	e4pj3A3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_11_1	ECOD (1.6)
A	AAA_12	e4pj3A4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: AAA_12	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21144	Intron-binding protein aquarius insert domain (Aquarius_N_3rd)	Intron-binding protein aquarius insert domain	This entry represents the insert domain of intron-binding protein aquarius, a splicing factor which links excision of introns from pre-mRNA with snoRP assembly [1,2].	Domain
A	PF13086	AAA domain (AAA_11)	AAA domain	This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.	Domain
A	PF21143	Intron-binding protein aquarius, beta-barrel (Aquarius_N_2nd)	Intron-binding protein aquarius, beta-barrel	This entry represents the beta-barrel domain found at the N-terminal of intron-binding protein aquarius, a splicing factor which links excision of introns from pre-mRNA with snoRP assembly [1,2].	Domain
A	PF13087	AAA domain (AAA_12)	AAA domain	This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins.	Domain
A	PF16399	Intron-binding protein aquarius N-terminal (Aquarius_N_1st)	Intron-binding protein aquarius N-terminal	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Intron-binding protein aquarius	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 RNA binding nucleic acid binding mRNA 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 single-stranded RNA binding nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity 3'-5' RNA helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome metabolic process cellular process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile macromolecule metabolic process RNA processing	cellular anatomical structure membrane membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle spliceosomal complex organelle ribonucleoprotein complex cellular anatomical structure membrane membrane-bounded organelle catalytic step 2 spliceosome protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle spliceosomal complex organelle ribonucleoprotein complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen U2-type spliceosomal complex U2-type catalytic step 2 spliceosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR048966	RNA helicase aquarius, beta-barrel	Domain
A	IPR048967	RNA helicase aquarius, insertion domain	Domain
A	IPR041677	DNA2/NAM7 helicase, helicase domain	Domain
A	IPR026300	CWF11 family	Family
A	IPR045055	DNA2/NAM7-like helicase	Family
A	IPR032174	RNA helicase aquarius, N-terminal domain	Domain
A	IPR041679	DNA2/NAM7 helicase-like, C-terminal	Domain
A	IPR047187	Upf1-like, C-terminal helicase domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O60306	atypical teratoid rhabdoid tumor hepatocellular carcinoma medulloblastoma psoriasis gastric cancer large cell medulloblastoma oligodendroglioma gastric carcinoma malignant mesothelioma ovarian cancer

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.