7K1B

CryoEM structure of DNA-PK catalytic subunit complexed with DNA (Complex II)

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08163	DNA-dependent protein kinase catalytic subunit, CC3 (DNAPKcs_CC3)	DNA-dependent protein kinase catalytic subunit, CC3	-	Repeat
A	PF02260	FATC domain (FATC)	FATC domain	-	Family
A	PF00454	Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)	Phosphatidylinositol 3- and 4-kinase	-	Family
A	PF20502	DNA-dependent protein kinase catalytic subunit, CC1/2 (DNAPKcs_CC1-2)	DNA-dependent protein kinase catalytic subunit, CC1/2	-	Repeat
A	PF19704	DNA-PKcs, CC5 (DNAPKcs_CC5)	DNA-PKcs, CC5	-	Repeat
A	PF02259	FAT domain (FAT)	FAT domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA-dependent protein kinase catalytic subunit	RNA binding binding U3 snoRNA binding organic cyclic compound binding snoRNA binding nucleic acid binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity DNA-dependent protein kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor RNA binding binding U3 snoRNA binding organic cyclic compound binding snoRNA binding nucleic acid binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity DNA-dependent protein kinase activity catalytic 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 binding protein domain specific binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding histone H2AXS139 kinase activity histone modifying activity histone kinase activity histone H2AX kinase activity protein serine kinase activity DNA binding double-stranded DNA binding histone H2AS1 kinase activity histone H2A kinase activity enzyme binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development heart development circulatory system development cellular developmental process hemopoiesis B cell activation cell activation cell development B cell lineage commitment mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process cell fate commitment leukocyte differentiation macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process protein destabilization regulation of protein stability biological regulation regulation of biological quality regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of response to stimulus positive regulation of metabolic process positive regulation of DNA repair regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of double-strand break repair via nonhomologous end joining DNA repair double-strand break repair regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of double-strand break repair via nonhomologous end joining double-strand break repair via nonhomologous end joining DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process positive regulation of double-strand break repair regulation of DNA repair positive regulation of DNA metabolic process regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of biological process negative regulation of phosphate metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process negative regulation of cellular process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process negative regulation of protein phosphorylation negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism innate immune response response to external biotic stimulus cell population proliferation regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation smooth muscle cell proliferation peptidyl-amino acid modification peptidyl-threonine modification peptidyl-threonine phosphorylation regulation of cell cycle phase transition DNA damage checkpoint signaling signaling negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic G1 DNA damage checkpoint signaling mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle signal transduction in response to DNA damage G1/S transition of mitotic cell cycle mitotic cell cycle phase transition immature B cell differentiation T cell differentiation in thymus T cell activation T cell differentiation T cell lineage commitment regulation of developmental process homeostatic process regulation of cell differentiation regulation of cell development positive regulation of developmental process positive regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process myeloid cell homeostasis erythrocyte homeostasis regulation of multicellular organismal development regulation of myeloid cell differentiation erythrocyte differentiation regulation of erythrocyte differentiation positive regulation of erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis homeostasis of number of cells reproductive process developmental process involved in reproduction programmed cell death involved in cell development ectopic germ cell programmed cell death peptidyl-serine modification peptidyl-serine phosphorylation double-strand break repair via alternative nonhomologous end joining telomere organization chromosome organization telomere maintenance cellular component organization organelle organization telomere capping cellular component organization or biogenesis maturation of 5.8S rRNA ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process biosynthetic process RNA processing rRNA metabolic process positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway regulation of signal transduction cGAS/STING signaling pathway immune response-activating signaling pathway positive regulation of immune response positive regulation of immune system process innate immune response-activating signaling pathway regulation of innate immune response negative regulation of cGAS/STING signaling pathway regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus regulation of response to external stimulus intracellular receptor signaling pathway negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of signaling positive regulation of innate immune response negative regulation of response to stimulus negative regulation of signal transduction negative regulation of immune system process regulation of cell communication regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation positive regulation of lymphocyte activation positive regulation of cell activation positive regulation of hemopoiesis positive regulation of leukocyte activation regulation of lymphocyte differentiation positive regulation of cell development positive regulation of multicellular organismal process positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of lymphocyte activation positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription immune system development somatic cell DNA recombination V(D)J recombination T cell receptor V(D)J recombination somatic diversification of T cell receptor genes somatic diversification of immune receptors DNA recombination somatic diversification of immune receptors via germline recombination within a single locus somatic recombination of T cell receptor gene segments pro-B cell differentiation lymphoid progenitor cell differentiation hematopoietic progenitor cell differentiation regulation of hematopoietic stem cell differentiation stem cell differentiation regulation of stem cell differentiation hematopoietic stem cell differentiation regulation of hematopoietic progenitor cell differentiation somitogenesis epithelium development chordate embryonic development segmentation anterior/posterior pattern specification pattern specification process embryo development tissue development regionalization anatomical structure morphogenesis embryo development ending in birth or egg hatching somite development anatomical structure formation involved in morphogenesis rhythmic process circadian rhythm regulation of circadian rhythm negative regulation of programmed cell death negative regulation of apoptotic process positive regulation of protein metabolic process positive regulation of translation post-transcriptional regulation of gene expression translation positive regulation of gene expression regulation of translation apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway regulation of epithelial cell proliferation epithelial cell proliferation response to ionizing radiation response to radiation response to abiotic stimulus response to gamma radiation platelet morphogenesis regulation of platelet formation cell morphogenesis regulation of cell morphogenesis positive regulation of platelet formation regulation of anatomical structure morphogenesis positive regulation of cell morphogenesis platelet formation cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to insulin cellular response to insulin stimulus cellular response to hormone stimulus immunoglobulin production somatic recombination of immunoglobulin gene segments production of molecular mediator of immune response somatic diversification of immunoglobulins immunoglobulin V(D)J recombination organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis protein-RNA complex organization cellular component assembly cytosolic ribosome assembly protein-containing complex assembly small-subunit processome assembly cytosolic small ribosomal subunit assembly ribosome assembly	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome preribosome cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome preribosome ribonucleoprotein complex small-subunit processome membrane-bounded organelle catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups DNA-dependent protein kinase complex serine/threonine protein kinase complex chromosome, telomeric region chromosomal region membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen nucleoplasm nonhomologous end joining complex intracellular protein-containing complex DNA repair complex DNA-dependent protein kinase-DNA ligase 4 complex protein-DNA complex
B [auth D], C [auth F]	DNA (5'-D(PGPCPAPTPGPCPTPCPTPAPCPTPGPCPTPTPCPGPAPTPAPTPCPG)-3')	-	-	-
D [auth G]	DNA (5'-D(PAPAPGPCPAPGPTPAPGPAPGPCPAPTPGPC)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016024	Armadillo-type fold	Homologous Superfamily
A	IPR003151	PIK-related kinase, FAT	Domain
A	IPR046803	DNA-dependent protein kinase catalytic subunit, CC1/2	Domain
A	IPR046804	DNA-PKcs, N-terminal	Domain
A	IPR045581	DNA-dependent protein kinase catalytic subunit, CC5	Domain
A	IPR003152	FATC domain	Domain
A	IPR012582	DNA-dependent protein kinase catalytic subunit, CC3	Domain
A	IPR011989	Armadillo-like helical	Homologous Superfamily
A	IPR018936	Phosphatidylinositol 3/4-kinase, conserved site	Conserved Site
A	IPR000403	Phosphatidylinositol 3-/4-kinase, catalytic domain	Domain
A	IPR050517	DNA Damage Response and Repair Kinase	Family
A	IPR036940	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily	Homologous Superfamily
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A	IPR037706	DNA-dependent protein kinase catalytic subunit, catalytic domain	Domain
A	IPR014009	PIK-related kinase	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P78527	severe combined immunodeficiency due to DNA-PKcs deficiency hepatic encephalopathy adenoid cystic carcinoma severe combined immunodeficiency Massive Hepatic Necrosis poisoning hepatic coma lung adenocarcinoma prostate cancer salivary gland adenoid cystic carcinoma squamous cell carcinoma lung cancer malignant colon neoplasm metastatic melanoma non-small cell lung carcinoma severe combined immunodeficiency due to DNA-PKcs deficiency hepatic encephalopathy adenoid cystic carcinoma severe combined immunodeficiency Massive Hepatic Necrosis poisoning hepatic coma lung adenocarcinoma prostate cancer salivary gland adenoid cystic carcinoma squamous cell carcinoma lung cancer malignant colon neoplasm metastatic melanoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm breast carcinoma squamous cell lung carcinoma glioblastoma large cell medulloblastoma lung disease myopathy osteosarcoma astrocytic tumor cancer psoriasis colorectal adenocarcinoma drug-induced liver injury medulloblastoma nasopharyngeal carcinoma ovarian cancer attention deficit hyperactivity disorder, inattentive type

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.