4BUJ | pdb_00004buj

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)
H	SCOP2B Superfamily	WD40 repeat-like	8039680	3001694	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	WD40 repeat-like	8039680	3001694	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	WD40 repeat-like	8039680	3001694	SCOP2B (2022-06-29)
C	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)
H	Cupredoxin_1	e4bujH2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Cupredoxin_1	ECOD (v294.1)
G		e4bujG1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F:	ECOD (v294.1)
D		e4bujD1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F:	ECOD (v294.1)
C		e4bujC1	A: a/b three-layered sandwiches	X: PRTase-like	H: PRTase-like	T: PRTase-like	F:	ECOD (v294.1)
F	PRMT5_TIM	e4bujF1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PRMT5_TIM	ECOD (v294.1)
B	PGDH_C	e4bujB1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: PGDH_C	ECOD (v294.1)
E	Ion_trans_2	e4bujE4	A: a/b three-layered sandwiches	X: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit	F: Ion_trans_2	ECOD (v294.1)
E	SHQ1-like_CS	e4bujE6	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: SHQ1-like_CS	ECOD (v294.1)
E	TPP_enzyme_C	e4bujE8	A: a/b three-layered sandwiches	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: TPP_enzyme_C	ECOD (v294.1)
A	Helicase_C	e4bujA1	A: a/b three-layered sandwiches	X: Sec63 N-terminal subdomain-like	H: Sec63 N-terminal subdomain-like	T: Sec63 N-terminal subdomain-like	F: Helicase_C	ECOD (v294.1)
A	DSHCT	e4bujA4	A: a/b three-layered sandwiches	X: Sec63 N-terminal subdomain-like	H: Sec63 N-terminal subdomain-like	T: Sec63 N-terminal subdomain-like	F: DSHCT	ECOD (v294.1)
A	Glyco_hydro_67N	e4bujA5	A: a/b three-layered sandwiches	X: Glutamine synthetase-like	H: ARM repeat	T: ARM repeat	F: Glyco_hydro_67N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	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)
D	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
C	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D, G, H	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
B, F	PF18833	Tetratricopeptide repeat (TPR_22)	Tetratricopeptide repeat	-	Repeat
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
A, E	PF17911	Ski2 N-terminal region (Ski2_N)	Ski2 N-terminal region	This region is the N-terminal extended region found in the Ski2 protein. The Ski complex is a conserved multiprotein assembly required for the cytoplasmic functions of the exosome, including RNA turnover, surveillance, and interference [1]. Ski2, Ski ...	This region is the N-terminal extended region found in the Ski2 protein. The Ski complex is a conserved multiprotein assembly required for the cytoplasmic functions of the exosome, including RNA turnover, surveillance, and interference [1]. Ski2, Ski3, and Ski8 assemble in a tetramer with 1:1:2 stoichiometry.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D, G, H	ANTIVIRAL PROTEIN SKI8	-	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 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 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 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 intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome intracellular membraneless organelle chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm protein-containing complex Ski complex
B, F	SUPERKILLER PROTEIN 3	-	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 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	protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm Ski complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
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 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
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	IPR051510	Superkiller complex protein 8	Family
C, D, G, H	IPR001680	WD40 repeat	Repeat
C, D, G, H	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	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
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	IPR050699	ATP-dependent RNA helicase SUPV3-like	Family
A, E	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, E	IPR016438	Circadian oscillator component FRH-like	Family
A, E	IPR040801	Ski2, N-terminal domain	Domain
A, E	IPR011545	DEAD/DEAH-box helicase domain	Domain
A, E	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.