Annotations: 6CNN

Cryo-EM structure of the human SK4/calmodulin channel complex in the Ca2+ bound state I

External Resource: Annotation

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
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	EF-hand	8033438	3001983	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	EF-hand	8033438	3001983	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	EF-hand	8033438	3001983	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	EF-hand	8033438	3001983	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Voltage-gated potassium channels	8093290	3000023	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Calmodulin binding domain (CaMBD)-like	8093288	3002034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Voltage-gated potassium channels	8093290	3000023	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Calmodulin binding domain (CaMBD)-like	8093288	3002034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Voltage-gated potassium channels	8093290	3000023	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Calmodulin binding domain (CaMBD)-like	8093288	3002034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Calmodulin binding domain (CaMBD)-like	8093288	3002034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Voltage-gated potassium channels	8093290	3000023	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)
H	TNF	e6cnnH1	A: beta barrels	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (v294.2)
G	TNF	e6cnnG1	A: beta barrels	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (v294.2)
F	TNF	e6cnnF1	A: beta barrels	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: TNF	ECOD (v294.2)
E	TBP	e6cnnE1	A: beta barrels	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: TBP	ECOD (v294.2)
D	MIF4G	e6cnnD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
C	MIF4G	e6cnnC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
B	MIF4G	e6cnnB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
A	MIF4G	e6cnnA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (utative)
G	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (utative)
F	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (utative)
E	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F, G, H	PF13499	EF-hand domain pair (EF-hand_7)	EF-hand domain pair		Domain
A, B, C, D	PF02888	Calmodulin binding domain (CaMBD)	Calmodulin binding domain	Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein cal ...	Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM) [1]. CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known [1]. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.	Domain
A, B, C, D	PF03530	Calcium-activated SK potassium channel (SK_channel)	Calcium-activated SK potassium channel	-	Family
A, B, C, D	PF07885	Ion channel (Ion_trans_2)	Ion channel	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	Calmodulin-1	cytoskeletal protein binding titin binding protein binding binding enzyme regulator activity protein phosphatase activator activity enzyme activator activity phosphatase activator activity molecular function activator activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity channel regulator activity ion channel regulator activity cytoskeletal protein binding titin binding protein binding binding enzyme regulator activity protein phosphatase activator activity enzyme activator activity phosphatase activator activity molecular function activator activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity channel regulator activity ion channel regulator activity calcium channel regulator activity transporter regulator activity molecular function inhibitor activity transporter inhibitor activity calcium channel inhibitor activity ion channel inhibitor activity channel inhibitor activity cyclase regulator activity cyclase activator activity adenylate cyclase regulator activity adenylate cyclase activator activity protein serine/threonine kinase activator activity kinase activator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity cation binding ion binding calcium ion binding metal ion binding small molecule binding transmembrane transporter binding kinase binding enzyme binding protein kinase binding calcium-dependent protein binding	organelle localization by membrane tethering localization organelle localization cellular process membrane docking heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation organelle localization by membrane tethering localization organelle localization cellular process membrane docking heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation regulation of multicellular organismal process regulation of biological quality heart contraction blood circulation regulation of heart rate regulation of localization regulation of calcium ion transport negative regulation of ion transmembrane transporter activity regulation of cellular process negative regulation of calcium ion transmembrane transporter activity transport negative regulation of monoatomic ion transport monoatomic ion transmembrane transport negative regulation of biological process negative regulation of ryanodine-sensitive calcium-release channel activity regulation of transmembrane transporter activity negative regulation of transport regulation of monoatomic ion transmembrane transport negative regulation of transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport intercellular transport negative regulation of monoatomic ion transmembrane transport negative regulation of release of sequestered calcium ion into cytosol negative regulation of cellular process monoatomic ion transport negative regulation of cation transmembrane transport monoatomic cation transport regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of transport regulation of release of sequestered calcium ion into cytosol regulation of monoatomic ion transport negative regulation of transporter activity negative regulation of molecular function establishment of localization negative regulation of calcium ion transport transmembrane transport regulation of molecular function release of sequestered calcium ion into cytosol regulation of transmembrane transport regulation of ryanodine-sensitive calcium-release channel activity regulation of monoatomic cation transmembrane transport negative regulation of calcium ion transmembrane transport calcium ion transmembrane transport response to stimulus response to metal ion response to chemical response to calcium ion sarcoplasmic reticulum calcium ion transport release of sequestered calcium ion into cytosol by sarcoplasmic reticulum release of sequestered calcium ion into cytosol by endoplasmic reticulum regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum negative regulation of voltage-gated calcium channel activity regulation of voltage-gated calcium channel activity negative regulation of high voltage-gated calcium channel activity cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation autophagosome membrane docking metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism cellular response to interferon-beta response to peptide response to interferon-beta response to cytokine cellular response to cytokine stimulus regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division cell division cell cycle regulation of cell cycle cell cycle process cellular response to stimulus cardiac muscle contraction intracellular signal transduction cell communication intracellular signaling cassette signal transduction regulation of cardiac muscle contraction muscle contraction regulation of striated muscle contraction calcium-mediated signaling regulation of muscle contraction signaling regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion striated muscle contraction regulation of cardiac muscle contraction by calcium ion signaling muscle system process regulation of muscle system process import into cell cellular localization presynaptic endocytosis vesicle-mediated transport vesicle-mediated transport in synapse establishment of localization in cell endocytosis cell communication by electrical coupling involved in cardiac conduction cell communication by electrical coupling regulation of cell communication by electrical coupling involved in cardiac conduction cardiac conduction regulation of cell communication cell communication involved in cardiac conduction regulation of cell communication by electrical coupling export across plasma membrane negative regulation of calcium ion export across plasma membrane regulation of calcium ion export across plasma membrane calcium ion export across plasma membrane export from cell biological process involved in interspecies interaction between organisms immune response response to other organism defense response response to type II interferon defense response to symbiont response to external stimulus cellular response to type II interferon response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus calcineurin-mediated signaling developmental process head development animal organ development brain development nervous system development substantia nigra development multicellular organism development central nervous system development midbrain development anatomical structure development neural nucleus development system development positive regulation of cell communication cell surface receptor signaling pathway via STAT positive regulation of signal transduction positive regulation of biological process positive regulation of receptor signaling pathway via STAT regulation of signal transduction positive regulation of receptor signaling pathway via JAK-STAT positive regulation of response to stimulus regulation of receptor signaling pathway via JAK-STAT positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway regulation of response to stimulus regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT positive regulation of signaling regulation of action potential regulation of cardiac muscle cell action potential action potential cardiac muscle cell action potential regulation of membrane potential G protein-coupled receptor signaling pathway modulation of chemical synaptic transmission long-term synaptic potentiation synaptic signaling regulation of synaptic plasticity trans-synaptic signaling cell-cell signaling positive regulation of synaptic transmission chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling detection of stimulus detection of chemical stimulus detection of calcium ion	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle cell projection intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton cytoplasm cytosol membrane-bounded organelle cell projection sperm midpiece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection protein-containing complex transmembrane transporter complex membrane membrane protein complex cation channel complex transporter complex calcium channel complex monoatomic ion channel complex axon synapse neuron projection axon terminus presynapse distal axon calyx of Held cell junction neuron projection terminus sarcomere contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex myelin sheath vesicle centrosome microtubule organizing center presynaptic cytosol cell periphery plasma membrane catalytic complex nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen voltage-gated potassium channel complex plasma membrane protein complex potassium channel complex extracellular region polymeric cytoskeletal fiber spindle microtubule microtubule
A, B, C, D	Intermediate conductance calcium-activated potassium channel protein 4	monoatomic cation transmembrane transporter activity calcium-activated cation channel activity gated channel activity monoatomic ion channel activity potassium ion transmembrane transporter activity potassium channel activity monoatomic ion-gated channel activity calcium-activated potassium channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity monoatomic cation channel activity passive transmembrane transporter activity intermediate conductance calcium-activated potassium channel activity channel activity monoatomic ion transmembrane transporter activity monoatomic cation transmembrane transporter activity calcium-activated cation channel activity gated channel activity monoatomic ion channel activity potassium ion transmembrane transporter activity potassium channel activity monoatomic ion-gated channel activity calcium-activated potassium channel activity ligand-gated channel activity ligand-gated monoatomic ion channel activity monoatomic cation channel activity passive transmembrane transporter activity intermediate conductance calcium-activated potassium channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity ligand-gated monoatomic cation channel activity metal ion transmembrane transporter activity transmembrane transporter activity protein phosphatase binding phosphatase binding protein binding binding enzyme binding small conductance calcium-activated potassium channel activity identical protein binding protein homodimerization activity protein dimerization activity calmodulin binding	regulation of calcium ion transport regulation of localization import into cell regulation of cellular process transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport calcium ion import into cytosol regulation of calcium ion transport regulation of localization import into cell regulation of cellular process transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport regulation of calcium ion transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport calcium ion import into cytosol monoatomic cation transport regulation of metal ion transport regulation of calcium ion import regulation of biological process calcium ion transmembrane import into cytosol regulation of transport regulation of monoatomic ion transport import across plasma membrane biological regulation establishment of localization inorganic cation import across plasma membrane transmembrane transport regulation of transmembrane transport calcium ion import across plasma membrane regulation of calcium ion import across plasma membrane inorganic ion import across plasma membrane cellular process regulation of monoatomic cation transmembrane transport calcium ion import calcium ion transmembrane transport potassium ion transmembrane transport potassium ion transport protein-containing complex organization protein homotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis response to stimulus defense response response to stress immune system process cellular response to stimulus positive regulation of cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of signal transduction positive regulation of T cell receptor signaling pathway signaling positive regulation of biological process regulation of antigen receptor-mediated signaling pathway regulation of signal transduction cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response regulation of T cell receptor signaling pathway T cell receptor signaling pathway regulation of response to stimulus regulation of immune response regulation of cell communication antigen receptor-mediated signaling pathway activation of immune response positive regulation of antigen receptor-mediated signaling pathway positive regulation of signaling macropinocytosis pinocytosis endocytosis vesicle-mediated transport stabilization of membrane potential regulation of biological quality regulation of membrane potential positive regulation of cation transmembrane transport regulation of potassium ion transport positive regulation of monoatomic ion transport positive regulation of transmembrane transport positive regulation of monoatomic ion transmembrane transport regulation of potassium ion transmembrane transport positive regulation of potassium ion transport positive regulation of transport positive regulation of potassium ion transmembrane transport	membrane-bounded organelle cellular anatomical structure organelle vesicle ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region membrane-bounded organelle cellular anatomical structure organelle vesicle ruffle cell leading edge plasma membrane membrane leading edge membrane plasma membrane bounded cell projection cell periphery cell projection ruffle membrane plasma membrane region cell projection membrane voltage-gated potassium channel complex protein-containing complex plasma membrane protein complex potassium channel complex membrane protein complex cation channel complex transporter complex transmembrane transporter complex monoatomic ion channel complex neuron projection somatodendritic compartment cell body neuronal cell body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR002048	EF-hand domain	Domain
E, F, G, H	IPR050230	Calmodulin/Myosin light chain/Troponin C-like	Family
E, F, G, H	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
E, F, G, H	IPR011992	EF-hand domain pair	Homologous Superfamily
A, B, C, D	IPR015449	Potassium channel, calcium-activated, SK	Family
A, B, C, D	IPR013099	Potassium channel domain	Domain
A, B, C, D	IPR036122	SK, calmodulin-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR004178	Calmodulin-binding domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F, G, H	: P0DP23	long QT syndrome catecholaminergic polymorphic ventricular tachycardia Alzheimer disease long QT syndrome 14 cocaine abuse Weight Gain cannabis dependence cocaine dependence phencyclidine abuse catecholaminergic polymorphic ventricular tachycardia 4 rheumatoid arthritis glioblastoma subependymal giant cell astrocytoma large cell medulloblastoma lung adenocarcinoma long QT syndrome catecholaminergic polymorphic ventricular tachycardia Alzheimer disease long QT syndrome 14 cocaine abuse Weight Gain cannabis dependence cocaine dependence phencyclidine abuse catecholaminergic polymorphic ventricular tachycardia 4 rheumatoid arthritis glioblastoma subependymal giant cell astrocytoma large cell medulloblastoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm astrocytic tumor myopathy osteosarcoma pituitary cancer Crohn disease primitive neuroectodermal tumor familial long QT syndrome schizophrenia lung cancer malignant ependymoma atypical teratoid rhabdoid tumor nasopharyngeal carcinoma ovarian cancer catecholaminergic polymorphic ventricular tachycardia 2 Pick disease plasma cell myeloma exocrine pancreatic carcinoma psoriasis sinusitis hepatocellular carcinoma ulcerative colitis lymphoplasmacytic lymphoma malignant glioma amyotrophic lateral sclerosis medulloblastoma breast cancer oligodendroglioma pilocytic astrocytoma
A, B, C, D	: O15554	dehydrated hereditary stomatocytosis 2 familial hemolytic anemia pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis tinea pedis amyotrophic lateral sclerosis Xerocytosis, hereditary breast carcinoma dermatophytosis of groin and perianal area interstitial lung disease malignant mesothelioma pancreatic intraductal papillary-mucinous carcinoma pityriasis versicolor sinusitis dehydrated hereditary stomatocytosis 2 familial hemolytic anemia pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia psoriasis tinea pedis amyotrophic lateral sclerosis Xerocytosis, hereditary breast carcinoma dermatophytosis of groin and perianal area interstitial lung disease malignant mesothelioma pancreatic intraductal papillary-mucinous carcinoma pityriasis versicolor sinusitis vulvovaginal candidiasis B-cell chronic lymphocytic leukemia hemolytic anemia lung adenocarcinoma malignant pancreatic neoplasm osteosarcoma pancreatic intraductal papillary-mucinous neoplasm tinea corporis breast cancer estrogen-receptor negative breast cancer interstitial cystitis malignant colon neoplasm oral candidiasis

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Transmembrane	Alpha-helical polytopic	Ion channel (VIC) superfamily	Calcium-activated SK potassium channel

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Potassium, Sodium, & Proton Ion-Selective	small-conductance Ca²⁺-activated K⁺ (SK) channel calmodulin complex, Ca- bound state I

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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.