5V8W | pdb_00005v8w

Crystal structure of human Integrator IntS9-IntS11 CTD complex

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)
H	YadA_head	e5v8wH1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Rubredoxin-related	T: Rubredoxin-related	F: YadA_head	ECOD (v294.1)
F	YadA_head	e5v8wF1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Rubredoxin-related	T: Rubredoxin-related	F: YadA_head	ECOD (v294.1)
D	YadA_head	e5v8wD1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Rubredoxin-related	T: Rubredoxin-related	F: YadA_head	ECOD (v294.1)
B	Cas9_RuvC	e5v8wB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: Cas9_RuvC	ECOD (v294.1)
G	YadA_head	e5v8wG1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Rubredoxin-related	T: Rubredoxin-related	F: YadA_head	ECOD (v294.1)
E	YadA_head	e5v8wE1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Rubredoxin-related	T: Rubredoxin-related	F: YadA_head	ECOD (v294.1)
C	YadA_head	e5v8wC1	A: a/b three-layered sandwiches	X: HAD domain-like	H: Rubredoxin-related	T: Rubredoxin-related	F: YadA_head	ECOD (v294.1)
A	IntS9_C	e5v8wA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: beta-propeller	T: 8-bladed	F: IntS9_C	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	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
A, C, E, G	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Integrator complex subunit 11	endonuclease activity nuclease activity catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity catalytic activity hydrolase activity cation binding ion binding binding metal ion binding small molecule binding	catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II RNA surveillance RNA catabolic process transcription initiation at RNA polymerase II promoter RNA polymerase II transcription initiation surveillance nuclear RNA surveillance primary metabolic process catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II RNA surveillance RNA catabolic process transcription initiation at RNA polymerase II promoter RNA polymerase II transcription initiation surveillance nuclear RNA surveillance primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation nucleobase-containing compound catabolic process biosynthetic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process snRNA 3'-end processing snRNA metabolic process snRNA processing RNA 3'-end processing RNA processing transcription elongation by RNA polymerase II regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process 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 macromolecule metabolic process regulation of gene expression DNA-templated transcription elongation regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	cellular anatomical structure extracellular region 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 cellular anatomical structure extracellular region 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 INTAC complex
A, C, E, G	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 catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II RNA surveillance RNA catabolic process transcription initiation at RNA polymerase II promoter RNA polymerase II transcription initiation surveillance nuclear RNA surveillance primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation nucleobase-containing compound catabolic process biosynthetic process nucleic acid catabolic process metabolic process macromolecule metabolic process snRNA 3'-end processing snRNA metabolic process snRNA processing RNA 3'-end processing RNA processing transcription elongation by RNA polymerase II regulation of primary metabolic process regulation of RNA metabolic process 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 macromolecule metabolic process regulation of gene expression DNA-templated transcription elongation regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process	cellular anatomical structure 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 cellular anatomical structure 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 INTAC complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR001279	Metallo-beta-lactamase	Domain
B, D, F, H	IPR022712	Beta-Casp domain	Domain
B, D, F, H	IPR050698	RNA Processing Metallo-Beta-Lactamase	Family
B, D, F, H	IPR041897	Integrator complex subunit 11, MBL-fold	Domain
B, D, F, H	IPR048662	Integrator complex subunit 11, C-terminal domain	Domain
B, D, F, H	IPR011108	Zn-dependent metallo-hydrolase, RNA specificity domain	Domain
B, D, F, H	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily
A, C, E, G	IPR027074	Integrator complex subunit 9	Family
A, C, E, G	IPR001279	Metallo-beta-lactamase	Domain
A, C, E, G	IPR022712	Beta-Casp domain	Domain
A, C, E, G	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily
A, C, E, G	IPR048660	Integrator complex subunit 9-like, C-terminal domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H	Pharos: Q5TA45	astrocytic tumor ulcerative colitis inflammatory bowel disease oligodendroglioma
A, C, E, G	Pharos: Q9NV88	astrocytic tumor medulloblastoma osteosarcoma

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.