4BUJ

Crystal structure of the S. cerevisiae Ski2-3-8 complex

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)
C	SCOP2B Superfamily	WD40 repeat-like	8039680	3001694	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	WD40 repeat-like	8039680	3001694	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	WD40 repeat-like	8039680	3001694	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	WD40 repeat-like	8039680	3001694	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)
A	F_UNCLASSIFIED	e4bujA3	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF08148	e4bujA4	A: alpha arrays	X: Sec63 N-terminal subdomain-like (From Topology)	H: Sec63 N-terminal subdomain-like (From Topology)	T: Sec63 N-terminal subdomain-like	F: PF08148	ECOD (1.6)
A	PF00270	e4bujA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00270	ECOD (1.6)
A	PF00271	e4bujA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00271	ECOD (1.6)
A	PF17911	e4bujA5	A: extended segments	X: Antiviral helicase Ski2 N-terminal extended region (From Topology)	H: Antiviral helicase Ski2 N-terminal extended region (From Topology)	T: Antiviral helicase Ski2 N-terminal extended region	F: PF17911	ECOD (1.6)
E	F_UNCLASSIFIED	e4bujE4	A: alpha arrays	X: HTH	H: HTH	T: winged	F: F_UNCLASSIFIED	ECOD (1.6)
E	PF08148	e4bujE8	A: alpha arrays	X: Sec63 N-terminal subdomain-like (From Topology)	H: Sec63 N-terminal subdomain-like (From Topology)	T: Sec63 N-terminal subdomain-like	F: PF08148	ECOD (1.6)
E	PF00270	e4bujE7	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00270	ECOD (1.6)
E	PF00271	e4bujE6	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00271	ECOD (1.6)
E	PF17911	e4bujE5	A: extended segments	X: Antiviral helicase Ski2 N-terminal extended region (From Topology)	H: Antiviral helicase Ski2 N-terminal extended region (From Topology)	T: Antiviral helicase Ski2 N-terminal extended region	F: PF17911	ECOD (1.6)
B	PF18833	e4bujB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF18833	ECOD (1.6)
F	PF18833	e4bujF1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: PF18833	ECOD (1.6)
C	PF00400	e4bujC1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00400	ECOD (1.6)
D	PF00400	e4bujD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00400	ECOD (1.6)
G	PF00400	e4bujG1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00400	ECOD (1.6)
H	PF00400	e4bujH2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: PF00400	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	1.10.3380.30	Mainly Alpha	Orthogonal Bundle	Sec63 N-terminal domain-like fold		CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	1.10.3380.30	Mainly Alpha	Orthogonal Bundle	Sec63 N-terminal domain-like fold		CATH (4.3.0)
C	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
D	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
G	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
H	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E	PF08148	DSHCT (NUC185) domain (DSHCT)	DSHCT (NUC185) domain	This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [1].	Domain
A, E	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, E	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
B, F	PF18833	Tetratricopeptide repeat (TPR_22)	Tetratricopeptide repeat	-	Repeat
C, D, G, H	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E	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
B, F	SUPERKILLER PROTEIN 3	-	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 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	protein-containing complex intracellular anatomical structure cytoplasm cellular anatomical entity Ski complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
C, D, G, H	ANTIVIRAL PROTEIN SKI8	-	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 cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis homologous recombination sexual reproduction reproductive process meiotic cell cycle process meiosis I meiotic nuclear division cell cycle reciprocal homologous recombination cell cycle process DNA recombination meiotic cell cycle organelle fission DNA metabolic process reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process 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 protein-DNA complex organization protein-DNA complex assembly nuclear-transcribed mRNA catabolic process, nonsense-mediated decay nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex cytoplasm Ski complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E	IPR048392	Exosome RNA helicase MTR4-like, stalk	Domain
A, E	IPR048727	Ski2, beta-barrel domain	Domain
A, E	IPR012961	ATP-dependent RNA helicase Ski2/MTR4, C-terminal	Domain
A, E	IPR001650	Helicase, C-terminal domain-like	Domain
A, E	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, E	IPR040801	Ski2, N-terminal domain	Domain
A, E	IPR016438	ATP-dependent RNA helicase SKI2-like	Family
A, E	IPR011545	DEAD/DEAH box helicase domain	Domain
A, E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, F	IPR040962	Tetratricopeptide-like repeat	Repeat
B, F	IPR039226	Ski3/TTC37	Family
B, F	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
B, F	IPR019734	Tetratricopeptide repeat	Repeat
C, D, G, H	IPR019775	WD40 repeat, conserved site	Conserved Site
C, D, G, H	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
C, D, G, H	IPR001680	WD40 repeat	Repeat
C, D, G, H	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	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.