4IMI | pdb_00004imi

Novel Modifications on C-terminal Domain of RNA Polymerase II can Fine- tune the Phosphatase Activity of Ssu72.

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Symplekin, N-terminal domain-like	8047136	4005463	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	ARM repeat-like	8093028	3000116	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	ARM repeat-like	8093028	3000116	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rhodanese/Cell cycle control phosphatase	8095912	3000320	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Rhodanese/Cell cycle control phosphatase	8095912	3000320	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	TraQ_transposon	e4imiA1	A: a/b three-layered sandwiches	X: immunoglobulin/albumin-binding domain-like	H: EGF-related	T: Complement control module/SCR domain	F: TraQ_transposon	ECOD (v294.1)
C	TraQ_transposon	e4imiC1	A: a/b three-layered sandwiches	X: immunoglobulin/albumin-binding domain-like	H: EGF-related	T: Complement control module/SCR domain	F: TraQ_transposon	ECOD (v294.1)
B	Peptidase_S26	e4imiB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)
C	1.25.10.10	Mainly Alpha	Alpha Horseshoe	Leucine-rich Repeat Variant	Leucine-rich Repeat Variant	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	6.10.140.550	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
D	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
D	6.10.140.550	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF11935	Symplekin/PTA1 N-terminal (SYMPK_PTA1_N)	Symplekin/PTA1 N-terminal	-	Repeat
B, D	PF04722	Ssu72-like protein (Ssu72)	Ssu72-like protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Symplekin	RNA binding binding nucleic acid binding	mRNA 3'-end processing co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway RNA metabolic process co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process mRNA 3'-end processing co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway RNA metabolic process co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process histone mRNA metabolic process mRNA 3'-end processing by stem-loop binding and cleavage	cell-cell junction cellular anatomical structure tight junction anchoring junction cell junction tricellular tight junction membrane-bounded organelle intracellular anatomical structure histone locus body nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen cell-cell junction cellular anatomical structure tight junction anchoring junction cell junction tricellular tight junction membrane-bounded organelle intracellular anatomical structure histone locus body nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen ribonucleoprotein granule intracellular organelle nuclear body nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen protein-containing complex nuclear protein-containing complex mRNA cleavage and polyadenylation specificity factor complex mRNA cleavage factor complex
B, D	CG14216	phosphoric ester hydrolase activity phosphoprotein phosphatase activity protein serine/threonine phosphatase activity RNA polymerase II CTD heptapeptide repeat modifying activity catalytic activity, acting on a protein RNA polymerase II CTD heptapeptide repeat phosphatase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity	mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing mRNA 3'-end processing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 3'-end processing metabolic process cellular process RNA processing macromolecule metabolic process DNA-templated transcription termination DNA-templated transcription transcription by RNA polymerase II termination of RNA polymerase II transcription	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle mRNA cleavage and polyadenylation specificity factor complex mRNA cleavage factor complex
E [auth F]	CTD	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR011989	Armadillo-like helical	Homologous Superfamily
A, C	IPR022075	Symplekin C-terminal	Domain
A, C	IPR016024	Armadillo-type fold	Homologous Superfamily
A, C	IPR021850	Symplekin/Pta1	Family
A, C	IPR032460	Symplekin/Pta1, N-terminal	Domain
B, D	IPR006811	RNA polymerase II subunit A	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth F]	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046
E [auth F]	TPO	Parent Component: THR RESID: AA0037 , AA0038 PSI-MOD : O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047

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.