Annotations: 9QL1

Cryo-EM structure of the CDK11B-cyclin L2-SAP30BP bound to OTS964 (conformation 2)

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth B]	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain
B [auth C]	PF21797	Cyclin-T2-like, C-terminal domain (CycT2-like_C)	Cyclin-T2-like, C-terminal domain	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P ...	This domain is found at the C-terminal end of human Cyclin-T2 (CycT2) and similar animal sequences. CycT2 is the regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFB). This domain adopts s cyclin box fold consisting of five helices and a short C-terminal helix [2].	Domain
A	PF07818	HCNGP-like protein (HCNGP)	HCNGP-like protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth B]	Cyclin-dependent kinase 11B	RNA binding binding nucleic acid binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding RNA binding binding nucleic acid binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups 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 protein serine/threonine kinase activity cyclin-dependent protein serine/threonine kinase activity cyclin-dependent protein kinase activity RNA polymerase II CTD heptapeptide repeat kinase activity RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat S5 kinase activity RNA polymerase II CTD heptapeptide repeat S2 kinase activity	cellular process cell cycle mitotic cell cycle apoptotic process cell death programmed cell death regulation of growth regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation growth regulation of cell growth cell growth cellular process cell cycle mitotic cell cycle apoptotic process cell death programmed cell death regulation of growth regulation of biological process regulation of cellular component organization regulation of cellular process biological regulation growth regulation of cell growth cell growth cellular component organization cellular component organization or biogenesis regulation of apoptotic process regulation of programmed cell death RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process metabolic process macromolecule metabolic process RNA processing mitotic sister chromatid cohesion chromosome organization sister chromatid cohesion centromeric sister chromatid cohesion organelle organization mitotic sister chromatid cohesion, centromeric cell cycle process RNA splicing regulation of mRNA splicing, via spliceosome regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of mRNA processing regulation of macromolecule metabolic process regulation of RNA splicing regulation of gene expression RNA splicing, via transesterification reactions mRNA splicing, via spliceosome regulation of macromolecule biosynthetic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process regulation of metabolic process DNA-templated transcription regulation of RNA biosynthetic process regulation of DNA-templated transcription protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process microtubule organizing center organization regulation of centrosome cycle regulation of cell cycle process microtubule cytoskeleton organization regulation of microtubule-based process centrosome cycle microtubule-based process regulation of cell cycle cytoskeleton organization promoter clearance during DNA-templated transcription RNA polymerase II promoter clearance transcription by RNA polymerase II	protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin-dependent protein kinase holoenzyme complex transferase complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cyclin L-CDK11 complex chromosome, centromeric region chromosome chromosomal region cytoplasm
B [auth C]	Cyclin-L2	enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity cyclin-dependent protein kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity	RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing macromolecule metabolic process regulation of cellular process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of mRNA processing regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of RNA splicing mRNA metabolic process regulation of gene expression RNA splicing, via transesterification reactions mRNA splicing, via spliceosome regulation of macromolecule biosynthetic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process regulation of metabolic process microtubule organizing center organization regulation of cellular component organization regulation of centrosome cycle regulation of cell cycle process microtubule cytoskeleton organization regulation of microtubule-based process cellular component organization organelle organization centrosome cycle microtubule-based process cell cycle cellular component organization or biogenesis regulation of cell cycle cytoskeleton organization cell cycle process DNA-templated transcription transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of DNA-templated transcription regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex cyclin L-CDK11 complex cyclin-dependent protein kinase holoenzyme complex transferase complex
A	SAP30-binding protein	enzyme regulator activity cyclin-dependent protein serine/threonine kinase regulator activity cyclin-dependent protein kinase regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity	biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus RNA splicing RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing macromolecule metabolic process regulation of cellular process regulation of mRNA splicing, via spliceosome mRNA processing regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biosynthetic process regulation of mRNA processing regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of RNA splicing mRNA metabolic process regulation of gene expression RNA splicing, via transesterification reactions mRNA splicing, via spliceosome regulation of macromolecule biosynthetic process RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process regulation of metabolic process DNA-templated transcription regulation of RNA biosynthetic process regulation of DNA-templated transcription	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body cellular anatomical structure nucleoplasm organelle lumen organelle membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B]	IPR000719	Protein kinase domain	Domain
C [auth B]	IPR045267	Cyclin-dependent kinase 11/PITSLRE, catalytic domain	Domain
C [auth B]	IPR050108	Cyclin-dependent kinase	Family
C [auth B]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C [auth B]	IPR008271	Serine/threonine-protein kinase, active site	Active Site
B [auth C]	IPR004367	Cyclin, C-terminal domain	Domain
B [auth C]	IPR006671	Cyclin, N-terminal	Domain
B [auth C]	IPR036915	Cyclin-like superfamily	Homologous Superfamily
B [auth C]	IPR043198	Cyclin/Cyclin-like subunit Ssn8	Family
B [auth C]	IPR013763	Cyclin-like domain	Domain
A	IPR012479	SAP30-binding protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C]	: Q96S94	astrocytic tumor lung adenocarcinoma medulloblastoma osteosarcoma Pick disease ulcerative colitis glioblastoma malignant ependymoma myopathy ovarian cancer progressive supranuclear palsy inflammatory bowel disease malignant mesothelioma oligodendroglioma pancreatic ductal adenocarcinoma astrocytic tumor lung adenocarcinoma medulloblastoma osteosarcoma Pick disease ulcerative colitis glioblastoma malignant ependymoma myopathy ovarian cancer progressive supranuclear palsy inflammatory bowel disease malignant mesothelioma oligodendroglioma pancreatic ductal adenocarcinoma psoriasis
A	: Q9UHR5	schizophrenia malignant ependymoma osteosarcoma Sjogren syndrome ovarian cancer

Protein Modification Annotation

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

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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.