4DGL

Crystal Structure of the CK2 Tetrameric Holoenzyme

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4dglb_	Small proteins	Rubredoxin-like	Casein kinase II beta subunit	Casein kinase II beta subunit	Casein kinase II beta subunit	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4dgla_	Small proteins	Rubredoxin-like	Casein kinase II beta subunit	Casein kinase II beta subunit	Casein kinase II beta subunit	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4dglc_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Protein kinase CK2, alpha subunit	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4dgld_	Alpha and beta proteins (a+b)	Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	Protein kinases, catalytic subunit	Protein kinase CK2, alpha subunit	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Casein kinase II beta subunit	8039162	3001271	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Casein kinase II beta subunit	8039162	3001271	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein kinase-like (PK-like)	8039449	3000066	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Protein kinase-like (PK-like)	8039449	3000066	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)
B	CK_II_beta	e4dglB1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Casein kinase II beta subunit	F: CK_II_beta	ECOD (1.6)
A	CK_II_beta	e4dglA1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Casein kinase II beta subunit	F: CK_II_beta	ECOD (1.6)
C	Pkinase_Tyr	e4dglC1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)
D	Pkinase_Tyr	e4dglD2	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Pkinase_Tyr	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.1820.10	Mainly Alpha	Orthogonal Bundle	protein kinase ck2 holoenzyme, chain C, domain 1	protein kinase ck2 holoenzyme, chain C, domain 1	CATH (4.3.0)
B	2.20.25.20	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
A	1.10.1820.10	Mainly Alpha	Orthogonal Bundle	protein kinase ck2 holoenzyme, chain C, domain 1	protein kinase ck2 holoenzyme, chain C, domain 1	CATH (4.3.0)
A	2.20.25.20	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
C	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
C	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
D	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)
D	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01214	Casein kinase II regulatory subunit (CK_II_beta)	Casein kinase II regulatory subunit	-	Domain
C, D	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Casein kinase II subunit beta	protein binding binding protein domain specific binding signaling receptor binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding protein-containing complex binding chromatin binding protein-macromolecule adaptor activity molecular adaptor activity protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein binding binding protein domain specific binding signaling receptor binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding protein-containing complex binding chromatin binding protein-macromolecule adaptor activity molecular adaptor activity protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups enzyme regulator activity molecular function regulator activity protein kinase regulator activity kinase regulator activity cation binding ion binding metal ion binding small molecule binding identical protein binding	cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process positive regulation of signal transduction response to stimulus signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction enzyme-linked receptor protein signaling pathway positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway biological regulation positive regulation of intracellular signal transduction positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway SMAD protein signal transduction regulation of response to stimulus regulation of cell communication cellular process regulation of SMAD protein signal transduction positive regulation of SMAD protein signal transduction positive regulation of signaling cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis developmental process multicellular organismal process epithelium development endothelium development tube development morphogenesis of an endothelium endothelial tube morphogenesis morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis multicellular organism development tube morphogenesis anatomical structure development epithelial tube morphogenesis organonitrogen compound metabolic process protein phosphorylation phosphorylation cellular metabolic process primary metabolic process organic substance metabolic process macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process metabolic process peptidyl-threonine modification protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process peptidyl-threonine phosphorylation regulation of molecular function regulation of DNA binding regulation of binding response to organic substance response to cytokine hormone-mediated signaling pathway cytokine-mediated signaling pathway cellular response to endogenous stimulus response to hormone cellular response to cytokine stimulus cellular response to organic substance cellular response to hormone stimulus response to endogenous stimulus adiponectin-activated signaling pathway cellular response to chemical stimulus response to chemical negative regulation of locomotion regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration negative regulation of biological process negative regulation of endothelial cell migration negative regulation of blood vessel endothelial cell migration tissue migration negative regulation of epithelial cell migration ameboidal-type cell migration regulation of cell migration negative regulation of cellular process blood vessel endothelial cell migration regulation of endothelial cell migration epithelial cell migration cell migration regulation of multicellular organismal process cell motility regulation of epithelial cell migration locomotion negative regulation of cell migration epithelium migration regulation of locomotion negative regulation of cell motility negative regulation of multicellular organismal process negative regulation of viral process regulation of viral process regulation of viral life cycle negative regulation of viral life cycle viral process viral life cycle symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host cell PML body symbiont-mediated disruption of host cellular anatomical entity disruption of anatomical structure in another organism negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation Wnt signaling pathway positive regulation of activin receptor signaling pathway activin receptor signaling pathway transforming growth factor beta receptor superfamily signaling pathway regulation of activin receptor signaling pathway	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle nucleus nucleoplasm nuclear lumen protein-containing complex protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen protein kinase complex transferase complex, transferring phosphorus-containing groups protein kinase CK2 complex catalytic complex serine/threonine protein kinase complex transferase complex intracellular protein-containing complex nuclear body PML body
C, D	Casein kinase II subunit alpha	kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups Hsp90 protein binding protein binding binding heat shock protein binding catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor adenyl ribonucleotide binding nucleotide binding kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups Hsp90 protein binding protein binding binding heat shock protein binding catalytic activity, acting on a protein protein kinase activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein serine/threonine kinase activity identical protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of biological process regulation of growth regulation of cellular process regulation of cellular component organization positive regulation of biological process biological regulation growth positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular component organization or biogenesis positive regulation of cellular process negative regulation of hydrolase activity negative regulation of proteolysis regulation of catalytic activity negative regulation of biological process negative regulation of catalytic activity regulation of programmed cell death negative regulation of endopeptidase activity regulation of primary metabolic process negative regulation of peptidase activity regulation of cysteine-type endopeptidase activity involved in apoptotic process organic substance metabolic process regulation of proteolysis proteolysis regulation of endopeptidase activity negative regulation of cellular process negative regulation of cysteine-type endopeptidase activity involved in apoptotic process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of cysteine-type endopeptidase activity organonitrogen compound metabolic process negative regulation of programmed cell death regulation of protein metabolic process regulation of apoptotic process negative regulation of metabolic process regulation of peptidase activity negative regulation of molecular function primary metabolic process regulation of macromolecule metabolic process cell death regulation of molecular function negative regulation of apoptotic process regulation of hydrolase activity negative regulation of cysteine-type endopeptidase activity metabolic process macromolecule metabolic process apoptotic process regulation of metabolic process programmed cell death cellular biosynthetic process organonitrogen compound biosynthetic process negative regulation of cellular metabolic process post-transcriptional regulation of gene expression negative regulation of translation organic substance biosynthetic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process gene expression translation macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of protein stability regulation of biological quality protein stabilization chaperone-mediated protein folding protein maturation protein folding catabolic process negative regulation of proteolysis involved in protein catabolic process proteolysis involved in protein catabolic process regulation of ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process negative regulation of ubiquitin-dependent protein catabolic process organonitrogen compound catabolic process negative regulation of catabolic process regulation of catabolic process protein catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process positive regulation of protein metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process protein phosphorylation phosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process peptidyl-threonine modification protein modification process phosphorus metabolic process peptidyl-threonine phosphorylation signaling signal transduction cell communication cell cycle cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation negative regulation of signaling regulation of signal transduction negative regulation of cell communication negative regulation of apoptotic signaling pathway regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction apoptotic signaling pathway regulation of response to stimulus regulation of cell communication regulation of apoptotic signaling pathway positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway cell surface receptor signaling pathway regulation of Wnt signaling pathway positive regulation of signaling macroautophagy autophagy positive regulation of cellular metabolic process regulation of autophagy positive regulation of aggrephagy cellular catabolic process aggrephagy positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of autophagy regulation of aggrephagy regulation of macroautophagy regulation of cellular catabolic process positive regulation of cellular catabolic process symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont-mediated disruption of host cell PML body symbiont-mediated disruption of host cellular anatomical entity disruption of anatomical structure in another organism rhythmic process regulation of chromosome segregation regulation of cell cycle process chromosome separation regulation of chromosome separation regulation of cell cycle chromosome segregation cell cycle process peptidyl-serine modification peptidyl-serine phosphorylation double-strand break repair DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA repair	membrane-bounded organelle protein-containing complex intracellular anatomical structure Sin3-type complex nucleus membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex chromosome intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm non-membrane-bounded organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure Sin3-type complex nucleus membrane-enclosed lumen nuclear chromosome nuclear protein-containing complex chromosome intracellular organelle lumen histone deacetylase complex intracellular organelle nucleoplasm non-membrane-bounded organelle catalytic complex protein-DNA complex chromatin intracellular membrane-bounded organelle cellular anatomical entity organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen cytoplasm cytosol cell periphery plasma membrane membrane protein kinase complex transferase complex, transferring phosphorus-containing groups protein kinase CK2 complex serine/threonine protein kinase complex transferase complex intracellular protein-containing complex nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000704	Casein kinase II, regulatory subunit	Family
A, B	IPR016149	Casein kinase II, regulatory subunit, N-terminal	Homologous Superfamily
A, B	IPR035991	Casein kinase II subunit beta-like	Homologous Superfamily
C, D	IPR045216	Casein Kinase 2, subunit alpha	Family
C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
C, D	IPR000719	Protein kinase domain	Domain
C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P67870	squamous cell carcinoma adult T-cell leukemia/lymphoma skin neoplasm skin cancer systemic lupus erythematosus acute T cell leukemia cancer Crohn disease Epileptic encephalopathy intellectual disability lung carcinoma rheumatoid arthritis cervical cancer cutaneous lupus erythematosus Hashimoto thyroiditis squamous cell carcinoma adult T-cell leukemia/lymphoma skin neoplasm skin cancer systemic lupus erythematosus acute T cell leukemia cancer Crohn disease Epileptic encephalopathy intellectual disability lung carcinoma rheumatoid arthritis cervical cancer cutaneous lupus erythematosus Hashimoto thyroiditis laryngeal squamous cell carcinoma membranous glomerulonephritis squamous cell lung carcinoma autism spectrum disorder chronic obstructive pulmonary disease epilepsy hypertensive disorder lung adenocarcinoma psoriatic arthritis
C, D	Pharos: P68400	squamous cell carcinoma adult T-cell leukemia/lymphoma Okur-Chung neurodevelopmental syndrome skin cancer intellectual disability skin neoplasm acute T cell leukemia large cell medulloblastoma medulloblastoma osteosarcoma rheumatoid arthritis lung cancer non-small cell lung carcinoma ovarian cancer Malformations of Cortical Development squamous cell carcinoma adult T-cell leukemia/lymphoma Okur-Chung neurodevelopmental syndrome skin cancer intellectual disability skin neoplasm acute T cell leukemia large cell medulloblastoma medulloblastoma osteosarcoma rheumatoid arthritis lung cancer non-small cell lung carcinoma ovarian cancer Malformations of Cortical Development pancreatic intraductal papillary-mucinous neoplasm

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.