4A4K | pdb_00004a4k

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)
E [auth I]	ROQ_II	e4a4kI1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: HTH	T: Three-helical HTH	F: ROQ_II	ECOD (v294.1)
E [auth I]	Ig_3	e4a4kI2	A: a/b three-layered sandwiches	X: Type II ABC importer transmembrane domain fold	H: DNA mismatch repair protein MutL regulatory subdomain	T: DNA mismatch repair protein MutL regulatory subdomain	F: Ig_3	ECOD (v294.1)
D [auth G]	ROQ_II	e4a4kG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: HTH	T: Three-helical HTH	F: ROQ_II	ECOD (v294.1)
D [auth G]	MshEN	e4a4kG2	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: MshEN	ECOD (v294.1)
C [auth E]	ROQ_II	e4a4kE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: HTH	T: Three-helical HTH	F: ROQ_II	ECOD (v294.1)
C [auth E]	Fer4, Fer4_7, Fer4_10	e4a4kE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Aha1/BPI domain-like	F: Fer4, Fer4_7, Fer4_10	ECOD (v294.1)
B [auth C]	ROQ_II	e4a4kC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: HTH	T: Three-helical HTH	F: ROQ_II	ECOD (v294.1)
B [auth C]		e4a4kC2	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F:	ECOD (v294.1)
A		e4a4kA1	A: a/b three-layered sandwiches	X: avirulence protein AvrPiz-t homologs	H: avirulence protein AvrPiz-t homologs	T: avirulence protein AvrPiz-t homologs	F:	ECOD (v294.1)
A	Glyco_hydro_3_C	e4a4kA2	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: Glyco_hydro_3_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)
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)

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

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 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 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 nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic 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 negative regulation of metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic 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 negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression 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 nuclear-transcribed mRNA catabolic process, non-stop decay regulation of protein metabolic process translation protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of translation protein metabolic process biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus nuclear-transcribed mRNA catabolic process, nonsense-mediated decay nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	cellular anatomical structure intracellular anatomical structure cytoplasm 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]	IPR050699	ATP-dependent RNA helicase SUPV3-like	Family
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]	IPR016438	Circadian oscillator component FRH-like	Family
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]	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 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.