4A4K

Crystal structure of the S. cerevisiae Ski2 insertion domain

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	KOG0947_2nd	e4a4kA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG0947_2nd	ECOD (1.6)
A	rRNA_proc-arch_3rd	e4a4kA2	A: extended segments	X: Helical arch in Ski2-like helicases (From Topology)	H: Helical arch in Ski2-like helicases (From Topology)	T: Helical arch in Ski2-like helicases	F: rRNA_proc-arch_3rd	ECOD (1.6)
E [auth I]	KOG0947_2nd	e4a4kI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG0947_2nd	ECOD (1.6)
E [auth I]	rRNA_proc-arch_3rd	e4a4kI2	A: extended segments	X: Helical arch in Ski2-like helicases (From Topology)	H: Helical arch in Ski2-like helicases (From Topology)	T: Helical arch in Ski2-like helicases	F: rRNA_proc-arch_3rd	ECOD (1.6)
B [auth C]	KOG0947_2nd	e4a4kC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG0947_2nd	ECOD (1.6)
B [auth C]	rRNA_proc-arch_3rd	e4a4kC2	A: extended segments	X: Helical arch in Ski2-like helicases (From Topology)	H: Helical arch in Ski2-like helicases (From Topology)	T: Helical arch in Ski2-like helicases	F: rRNA_proc-arch_3rd	ECOD (1.6)
C [auth E]	KOG0947_2nd	e4a4kE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG0947_2nd	ECOD (1.6)
C [auth E]	rRNA_proc-arch_3rd	e4a4kE2	A: extended segments	X: Helical arch in Ski2-like helicases (From Topology)	H: Helical arch in Ski2-like helicases (From Topology)	T: Helical arch in Ski2-like helicases	F: rRNA_proc-arch_3rd	ECOD (1.6)
D [auth G]	KOG0947_2nd	e4a4kG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOG0947_2nd	ECOD (1.6)
D [auth G]	rRNA_proc-arch_3rd	e4a4kG2	A: extended segments	X: Helical arch in Ski2-like helicases (From Topology)	H: Helical arch in Ski2-like helicases (From Topology)	T: Helical arch in Ski2-like helicases	F: rRNA_proc-arch_3rd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1500.20	Mainly Alpha	Up-down Bundle	YheA-like fold		CATH (4.3.0)
A	2.30.30.1160	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
E [auth I]	1.20.1500.20	Mainly Alpha	Up-down Bundle	YheA-like fold		CATH (4.3.0)
E [auth I]	2.30.30.1160	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B [auth C]	1.20.1500.20	Mainly Alpha	Up-down Bundle	YheA-like fold		CATH (4.3.0)
B [auth C]	2.30.30.1160	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C [auth E]	1.20.1500.20	Mainly Alpha	Up-down Bundle	YheA-like fold		CATH (4.3.0)
C [auth E]	2.30.30.1160	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D [auth G]	1.20.1500.20	Mainly Alpha	Up-down Bundle	YheA-like fold		CATH (4.3.0)
D [auth G]	2.30.30.1160	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth E], D [auth G], E [auth I]	PF21409	Ski2, beta-barrel domain (Ski2_beta-barrel)	Ski2, beta-barrel domain	Ski2 from yeast is an helicase with an overall similar structure to MTR4 proteins. It has an arch domain with an helical stalk/elbow (Pfam:PF21408) that flanks a beta-barrel (referred to as the KOW module in MTR4 homologues). This entry represents th ...	Ski2 from yeast is an helicase with an overall similar structure to MTR4 proteins. It has an arch domain with an helical stalk/elbow (Pfam:PF21408) that flanks a beta-barrel (referred to as the KOW module in MTR4 homologues). This entry represents the beta-barrel of Ski2 which does not have the KOW motif and is tightly packed against the helical stalk [1,2].	Domain
A, B [auth C], C [auth E], D [auth G], E [auth I]	PF21408	Exosome RNA helicase MTR4-like, stalk (MTR4-like_stalk)	Exosome RNA helicase MTR4-like, stalk	Exosome RNA helicase MTR4 is a conserved RNA helicase that functions together with the nuclear exosome and it is involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclear RNA surveillance pathways involv ...	Exosome RNA helicase MTR4 is a conserved RNA helicase that functions together with the nuclear exosome and it is involved in processing of structured RNAs, including snRNAs and snoRNAs. It also plays a role in nuclear RNA surveillance pathways involving the so-called TRAMP complex [1,2]. It contains an arch domain, required for proper 5.8S rRNA processing, and appears to function independently of canonical helicase activity [3]. The arch domain comprises an helical stalk/elbow that flanks a KOW module which adopts a beta-barrel fold. This entry represents the helical stalk found at the N-terminal of KOW beta-barrel from MTR4 [1-3]. This entry also includes Ski2-like helicases which have an overall similar structure to MTR4 proteins. However, Ski2 from yeast does not have the KOW motif and the beta-barrel is tightly packed against the helical stalk [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth E], D [auth G], E [auth I]	ANTIVIRAL HELICASE SKI2	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 DNA binding nucleic acid binding RNA 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 catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA	regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of cellular process catabolic process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process organic substance metabolic process organic substance biosynthetic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation nuclear-transcribed mRNA catabolic process, non-stop decay regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process negative regulation of cellular biosynthetic process nucleic acid metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process regulation of cellular biosynthetic process regulation of gene expression organic cyclic compound metabolic process negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process organic substance catabolic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression protein metabolic process organonitrogen compound metabolic process regulation of protein metabolic process translation regulation of translation biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus response to virus nuclear-transcribed mRNA catabolic process, nonsense-mediated decay nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	intracellular anatomical structure cytoplasm cellular anatomical entity protein-containing complex Ski complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR048392	Exosome RNA helicase MTR4-like, stalk	Domain
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR048727	Ski2, beta-barrel domain	Domain
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR012961	ATP-dependent RNA helicase Ski2/MTR4, C-terminal	Domain
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR001650	Helicase, C-terminal domain-like	Domain
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR040801	Ski2, N-terminal domain	Domain
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR016438	ATP-dependent RNA helicase SKI2-like	Family
A, B [auth C], C [auth E], D [auth G], E [auth I]	IPR011545	DEAD/DEAH box helicase domain	Domain
A, B [auth C], C [auth E], D [auth G], E [auth I]	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.