3D9O

Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3d9oa1	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	RNA Polymerase II carboxy-terminal domain (CTD)-interacting (CID) domain (RPR domain)	SCAF8	man (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3d9oa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	man (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3d9ob1	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	RNA Polymerase II carboxy-terminal domain (CTD)-interacting (CID) domain (RPR domain)	SCAF8	man (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3d9ob2	Artifacts	Tags	Tags	Tags	C-terminal Tags	man (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth Z]	d3d9oz_	Peptides	RNA polymerase II fragments	RNA polymerase II fragments	RNA polymerase II fragments	RNA polymerase II carboxy-terminal domain (CTD) peptide	( ) [TaxId: ], (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	ENTH/VHS domain-like	8053989	3000164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ENTH/VHS domain-like	8053989	3000164	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	CTD_bind	e3d9oA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: CTD_bind	ECOD (1.6)
B	CTD_bind	e3d9oB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: CTD_bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF04818	CID domain (CID)	CID domain	-	Repeat
C [auth Z]	PF05001	RNA polymerase Rpb1 C-terminal repeat (RNA_pol_Rpb1_R)	RNA polymerase Rpb1 C-terminal repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	RNA-binding protein 16	RNA binding binding nucleic acid binding mRNA binding basal transcription machinery binding RNA polymerase binding protein binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding phosphoprotein binding RNA polymerase II C-terminal domain binding RNA polymerase II C-terminal domain phosphoserine binding RNA binding binding nucleic acid binding mRNA binding basal transcription machinery binding RNA polymerase binding protein binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase core enzyme binding enzyme binding phosphoprotein binding RNA polymerase II C-terminal domain binding RNA polymerase II C-terminal domain phosphoserine binding phosphoserine residue binding protein phosphorylated amino acid binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription termination nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription termination nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process termination of RNA polymerase II transcription regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of DNA-templated transcription, elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation regulation of macromolecule metabolic process positive regulation of RNA metabolic process regulation of gene expression DNA-templated transcription elongation positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of termination of DNA-templated transcription negative regulation of biological process protein-containing complex disassembly negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled regulation of protein-containing complex disassembly negative regulation of RNA biosynthetic process regulation of termination of RNA polymerase II transcription, poly(A)-coupled negative regulation of nucleobase-containing compound metabolic process cellular component disassembly regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription termination of RNA polymerase II transcription, poly(A)-coupled negative regulation of cellular component organization negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of macromolecule biosynthetic process regulation of termination of DNA-templated transcription negative regulation of RNA metabolic process regulation of termination of RNA polymerase II transcription regulation of cellular component organization cellular component organization negative regulation of protein-containing complex disassembly negative regulation of cellular process cellular component organization or biogenesis negative regulation of macromolecule metabolic process protein-containing complex organization negative regulation of termination of RNA polymerase II transcription negative regulation of biosynthetic process	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex mRNA cleavage factor complex intracellular membrane-bounded organelle membrane-enclosed lumen intracellular organelle lumen organelle lumen nuclear periphery membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex mRNA cleavage factor complex intracellular membrane-bounded organelle membrane-enclosed lumen intracellular organelle lumen organelle lumen nuclear periphery nuclear lumen nuclear matrix cytoplasm nucleoplasm
C [auth Z]	CTD-PEPTIDE	5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups hydrolase activity extracellular matrix binding binding microfibril binding RNA binding 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity RNA-dependent RNA polymerase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups hydrolase activity extracellular matrix binding binding microfibril binding RNA binding nucleic acid binding chromatin binding promoter-specific chromatin binding cation binding magnesium ion binding ion binding metal ion binding small molecule binding DNA binding protein binding kinase binding enzyme binding DNA-directed 5'-3' RNA polymerase activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding transition metal ion binding zinc ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process DNA-templated transcription termination regulation of cellular process positive regulation of biological process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process RNA processing positive regulation of cellular process regulation of biosynthetic process RNA splicing regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of RNA splicing regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of RNA splicing regulation of metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen cytoplasm membraneless organelle intracellular membraneless organelle chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR051485	SR-related and CTD-associated factor	Family
A, B	IPR008942	ENTH/VHS	Homologous Superfamily
A, B	IPR000504	RNA recognition motif domain	Domain
A, B	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	Homologous Superfamily
A, B	IPR034370	SCAF8, RNA recognition motif	Domain
A, B	IPR006569	CID domain	Domain
A, B	IPR035979	RNA-binding domain superfamily	Homologous Superfamily
C [auth Z]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
C [auth Z]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
C [auth Z]	IPR007075	RNA polymerase Rpb1, domain 6	Domain
C [auth Z]	IPR000684	RNA polymerase II, heptapeptide repeat, eukaryotic	Repeat
C [auth Z]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
C [auth Z]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
C [auth Z]	IPR006592	RNA polymerase, N-terminal	Domain
C [auth Z]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
C [auth Z]	IPR007073	RNA polymerase Rpb1, domain 7	Domain
C [auth Z]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
C [auth Z]	IPR038593	RNA polymerase Rpb1, domain 7 superfamily	Homologous Superfamily
C [auth Z]	IPR000722	RNA polymerase, alpha subunit	Domain
C [auth Z]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
C [auth Z]	IPR007080	RNA polymerase Rpb1, domain 1	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9UPN6	breast cancer ovarian cancer juvenile dermatomyositis myopathy
C [auth Z]	Pharos: P24928	acute myeloid leukemia central nervous system cancer metabolic syndrome X astrocytic tumor diabetes mellitus osteosarcoma atrial fibrillation IgA glomerulonephritis uterine corpus leiomyoma