7BFQ

Structure of the Integrator cleavage module with extended INTS4 and rigid body docked INTS9/11 CTD

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	PF21382	e7bfqA3	A: a+b two layers	X: TBP-like	H: Integrator IntS9/IntS11 C-terminal domain (From Topology)	T: Integrator IntS9/IntS11 C-terminal domain	F: PF21382	ECOD (1.6)
A	PF16661	e7bfqA1	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: PF16661	ECOD (1.6)
A	PF10996	e7bfqA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF10996	ECOD (1.6)
B [auth C]	F_UNCLASSIFIED	e7bfqC1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth B]	PF07521,PF21386	e7bfqB1	A: a+b two layers	X: TBP-like	H: Integrator IntS9/IntS11 C-terminal domain (From Topology)	T: Integrator IntS9/IntS11 C-terminal domain	F: PF07521,PF21386	ECOD (1.6)
C [auth B]	PF16661	e7bfqB2	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: PF16661	ECOD (1.6)
C [auth B]	PF10996	e7bfqB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF10996	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21382	Integrator IntS9, C-terminal domain (IntS9_C)	Integrator IntS9, C-terminal domain	IntS9 is a component of integrator complex (INT) which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This is the C-terminal domain of IntS9 which interacts with the C-terminal of IntS1 ...	IntS9 is a component of integrator complex (INT) which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This is the C-terminal domain of IntS9 which interacts with the C-terminal of IntS11 (responsible for endonuclease activity of INT), a crucial interaction for the role of INT in snRNA 3'-end processing [1,2].	Domain
A	PF16661	Metallo-beta-lactamase superfamily domain (Lactamase_B_6)	Metallo-beta-lactamase superfamily domain	This family is part of the metallo-beta-lactamase superfamily.	Domain
A	PF10996	Beta-Casp domain (Beta-Casp)	Beta-Casp domain	The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains [1].	Domain
B [auth C]	PF20168	Sister chromatid cohesion protein PDS5 protein (PDS5)	Sister chromatid cohesion protein PDS5 protein	-	Repeat
C [auth B]	PF21386	Integrator IntS11, C-terminal domain (IntS11_C)	Integrator IntS11, C-terminal domain	IntS11 is the catalytic component of integrator complex (INT), which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This is the C-terminal domain of IntS11 which interacts with the C-te ...	IntS11 is the catalytic component of integrator complex (INT), which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing. This is the C-terminal domain of IntS11 which interacts with the C-terminal of IntS9 (Pfam:PF21382), which is a crucial interaction for the role of INT in snRNA 3'-end processing [1,2]. IntS11 is responsible of the endonuclease activity of INT [1-3].	Domain
C [auth B]	PF07521	Zn-dependent metallo-hydrolase RNA specificity domain (RMMBL)	Zn-dependent metallo-hydrolase RNA specificity domain	-	Motif
C [auth B]	PF16661	Metallo-beta-lactamase superfamily domain (Lactamase_B_6)	Metallo-beta-lactamase superfamily domain	This family is part of the metallo-beta-lactamase superfamily.	Domain
C [auth B]	PF10996	Beta-Casp domain (Beta-Casp)	Beta-Casp domain	The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Integrator complex subunit 9	-	cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to stimulus negative regulation of transforming growth factor beta receptor signaling pathway regulation of cellular process cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus response to stimulus negative regulation of signaling signaling cellular response to transforming growth factor beta stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication regulation of transforming growth factor beta receptor signaling pathway cellular response to endogenous stimulus negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus regulation of cellular response to transforming growth factor beta stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus biological regulation negative regulation of signal transduction response to transforming growth factor beta regulation of response to stimulus transforming growth factor beta receptor signaling pathway regulation of cell communication cellular process response to growth factor transforming growth factor beta receptor superfamily signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process snRNA 3'-end processing nucleobase-containing compound metabolic process organic cyclic compound metabolic process snRNA metabolic process organic substance metabolic process biosynthetic process snRNA processing organic substance biosynthetic process nucleic acid catabolic process metabolic process RNA 3'-end processing macromolecule metabolic process RNA processing transcription elongation by RNA polymerase II regulation of primary metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process regulation of cellular biosynthetic process regulation of gene expression DNA-templated transcription elongation organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle protein-containing complex integrator complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membrane-enclosed lumen intracellular organelle lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle protein-containing complex integrator complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B [auth C]	Integrator complex subunit 4	-	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process snRNA metabolic process organic substance metabolic process biosynthetic process snRNA processing organic substance biosynthetic process nucleic acid catabolic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process snRNA metabolic process organic substance metabolic process biosynthetic process snRNA processing organic substance biosynthetic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA processing transcription elongation by RNA polymerase II regulation of cellular process regulation of primary metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of biological process regulation of transcription elongation by RNA polymerase II biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process regulation of cellular biosynthetic process regulation of gene expression DNA-templated transcription elongation organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle protein-containing complex integrator complex nuclear protein-containing complex nucleoplasm
C [auth B]	Integrator complex subunit 11	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process snRNA metabolic process organic substance metabolic process biosynthetic process snRNA processing organic substance biosynthetic process nucleic acid catabolic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process snRNA metabolic process organic substance metabolic process biosynthetic process snRNA processing organic substance biosynthetic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA processing transcription elongation by RNA polymerase II regulation of cellular process regulation of primary metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of DNA-templated transcription elongation regulation of biological process regulation of transcription elongation by RNA polymerase II biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process regulation of cellular biosynthetic process regulation of gene expression DNA-templated transcription elongation organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	extracellular region extracellular space cellular anatomical entity blood microparticle intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle protein-containing complex integrator complex organelle nucleus nuclear protein-containing complex extracellular region extracellular space cellular anatomical entity blood microparticle intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle protein-containing complex integrator complex organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
D [auth U]	Unknown	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027074	Integrator complex subunit 9	Family
A	IPR001279	Metallo-beta-lactamase	Domain
A	IPR022712	Beta-Casp domain	Domain
A	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily
A	IPR048660	Integrator complex subunit 9-like, C-terminal domain	Domain
B [auth C]	IPR011989	Armadillo-like helical	Homologous Superfamily
B [auth C]	IPR016024	Armadillo-type fold	Homologous Superfamily
C [auth B]	IPR001279	Metallo-beta-lactamase	Domain
C [auth B]	IPR022712	Beta-Casp domain	Domain
C [auth B]	IPR041897	Integrator complex subunit 11, MBL-fold	Domain
C [auth B]	IPR048662	Integrator complex subunit 11, C-terminal domain	Domain
C [auth B]	IPR011108	Zn-dependent metallo-hydrolase, RNA specificity domain	Domain
C [auth B]	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9NV88	astrocytic tumor medulloblastoma osteosarcoma
B [auth C]	Pharos: Q96HW7	prostate cancer large cell medulloblastoma medulloblastoma Prostatic Neoplasms osteosarcoma Sjogren syndrome
C [auth B]	Pharos: Q5TA45	astrocytic tumor ulcerative colitis inflammatory bowel disease oligodendroglioma

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 R01GM133198.