Annotations: 9G8Q

40S-bound human SKI238 complex in the open state (Gatekeeping module)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Beta-Casp	e9g8qA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Beta-Casp	ECOD (v295.2)
D	Beta-Casp	e9g8qD1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Beta-Casp	ECOD (v295.2)
C	Beta-Casp	e9g8qC1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Beta-Casp	ECOD (v295.2)
B	Beta-Casp	e9g8qB1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Beta-Casp	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
C, D	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat
B	PF13181	Tetratricopeptide repeat (TPR_8)	Tetratricopeptide repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Helicase SKI2W	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 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 3'-5' RNA helicase activity RNA binding nucleic acid binding	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 disassembly ribosome disassembly translation protein biosynthetic process cellular component organization organelle organization organelle disassembly translational elongation cytoplasmic translation cytoplasmic translational elongation protein metabolic process cellular component organization or biogenesis rescue of stalled cytosolic ribosome 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 cytosol protein-containing complex Ski complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
C, D	WD repeat-containing protein 61	-	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 multicellular organismal process regulation of developmental process cellular developmental process cell development regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis transcription elongation by RNA polymerase II nucleobase-containing compound biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling cell communication signal transduction Wnt signaling pathway cellular component disassembly ribosome disassembly translation protein biosynthetic process cellular component organization organelle organization organelle disassembly translational elongation cytoplasmic translation cytoplasmic translational elongation protein metabolic process cellular component organization or biogenesis rescue of stalled cytosolic ribosome 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 cytosol intracellular organelle organelle euchromatin membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle euchromatin membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex transcription elongation factor complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm catalytic complex intracellular membrane-bounded organelle Cdc73/Paf1 complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen Ski complex
B	Superkiller complex 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 cellular component disassembly ribosome disassembly translation protein biosynthetic process cellular component organization organelle organization organelle disassembly translational elongation cytoplasmic translation cytoplasmic translational elongation protein metabolic process cellular component organization or biogenesis rescue of stalled cytosolic ribosome 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 cytosol intracellular organelle organelle euchromatin membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex Ski complex membrane-bounded organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle euchromatin membraneless organelle intracellular membraneless organelle chromatin chromosome protein-containing complex Ski complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR048392	Exosome RNA helicase MTR4-like, stalk	Domain
A	IPR012961	ATP-dependent RNA helicase Ski2/MTR4, C-terminal	Domain
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR050699	ATP-dependent RNA helicase SUPV3-like	Family
A	IPR025696	Exosome RNA helicase MTR4-like, beta-barrel domain	Domain
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR016438	Circadian oscillator component FRH-like	Family
A	IPR040801	Ski2, N-terminal domain	Domain
A	IPR011545	DEAD/DEAH-box helicase domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, D	IPR019775	WD40 repeat, conserved site	Conserved Site
C, D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
C, D	IPR051510	Superkiller complex protein 8	Family
C, D	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
C, D	IPR001680	WD40 repeat	Repeat
C, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B	IPR039226	Ski3/TTC37	Family
B	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
B	IPR019734	Tetratricopeptide repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: Q15477	trichohepatoenteric syndrome trichohepatoenteric syndrome 2 trichohepatoenteric syndrome 1 vitiligo age-related macular degeneration cervical cancer Hashimoto thyroiditis hypertensive disorder Malignant neoplasm of breast non-alcoholic fatty liver disease systemic lupus erythematosus wet macular degeneration atopic eczema colorectal cancer heart disease trichohepatoenteric syndrome trichohepatoenteric syndrome 2 trichohepatoenteric syndrome 1 vitiligo age-related macular degeneration cervical cancer Hashimoto thyroiditis hypertensive disorder Malignant neoplasm of breast non-alcoholic fatty liver disease systemic lupus erythematosus wet macular degeneration atopic eczema colorectal cancer heart disease intellectual disability membranous glomerulonephritis psoriatic arthritis ulcerative colitis autism spectrum disorder endometriosis hepatitis B virus infection lung carcinoma neuromyelitis optica squamous cell lung carcinoma
C, D	: Q9GZS3	acute myeloid leukemia ovarian cancer glioblastoma plasma cell myeloma lymphoplasmacytic lymphoma
B	: Q6PGP7	trichohepatoenteric syndrome trichohepatoenteric syndrome 1 adrenal cortex carcinoma intellectual disability malignant ependymoma oligodendroglioma psoriasis amyotrophic lateral sclerosis interstitial lung disease medulloblastoma osteosarcoma astrocytic tumor large cell medulloblastoma myopathy ovarian cancer

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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.