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- PDB-6feh: Solution Structure of CaM/Kv7.2-hAB Complex -

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Basic information

Entry
Database: PDB / ID: 6feh
TitleSolution Structure of CaM/Kv7.2-hAB Complex
Components
  • Calmodulin-1
  • Potassium voltage-gated channel subfamily KQT member 2,Potassium voltage-gated channel subfamily KQT member 2
KeywordsMETAL TRANSPORT / Voltage-gated potassium channel / Calmodulin / Complex / Transport / Calcium-signalling
Function / homology
Function and homology information


axon initial segment / Voltage gated Potassium channels / node of Ranvier / Interaction between L1 and Ankyrins / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor ...axon initial segment / Voltage gated Potassium channels / node of Ranvier / Interaction between L1 and Ankyrins / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / ankyrin binding / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / voltage-gated potassium channel activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / potassium ion transmembrane transport / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Platelet degranulation
Similarity search - Function
Potassium channel, voltage dependent, KCNQ2 / Ankyrin-G binding site / Ankyrin-G binding motif of KCNQ2-3 / Unstructured region on Potassium channel subunit alpha KvLQT2 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...Potassium channel, voltage dependent, KCNQ2 / Ankyrin-G binding site / Ankyrin-G binding motif of KCNQ2-3 / Unstructured region on Potassium channel subunit alpha KvLQT2 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / Ion transport domain / Ion transport protein / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Potassium voltage-gated channel subfamily KQT member 2 / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBernardo-Seisdedos, G. / Villarroel, A. / Millet, O.
Funding support Spain, 2items
OrganizationGrant numberCountry
Basque GovernmentElkartek BG2015 Spain
Spanish Ministry of Science and TechnologyCTQ2015-68756-R, BFU2015-66910-R and CSD2008-00005 Spain
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis and energy landscape for the Ca2+gating and calmodulation of the Kv7.2 K+channel.
Authors: Bernardo-Seisdedos, G. / Nunez, E. / Gomis, C. / Malo, C. / Villarroel, A. / Millet, O.
History
DepositionJan 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily KQT member 2,Potassium voltage-gated channel subfamily KQT member 2
B: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6126
Polymers30,4522
Non-polymers1604
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4120 Å2
ΔGint-72 kcal/mol
Surface area19150 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Potassium voltage-gated channel subfamily KQT member 2,Potassium voltage-gated channel subfamily KQT member 2 / KQT-like 2 / Neuroblastoma-specific potassium channel subunit alpha KvLQT2 / Voltage-gated ...KQT-like 2 / Neuroblastoma-specific potassium channel subunit alpha KvLQT2 / Voltage-gated potassium channel subunit Kv7.2


Mass: 13599.536 Da / Num. of mol.: 1 / Mutation: Del. R374-K493,Del. R374-K493
Source method: isolated from a genetically manipulated source
Details: ...Details: MSYYHHHHHHDYDIPTTENLYFQGAMGILGSGQKHFEKRRNPAAGLIQSAWRFYATNLSRTDLHSTWQYYERTVTVPMYRGLEDLTPGLKVSIRAVCVMRFLVSKRKFKESLRLD,MSYYHHHHHHDYDIPTTENLYFQGAMGILGSGQKHFEKRRNPAAGLIQSAWRFYATNLSRTDLHSTWQYYERTVTVPMYRGLEDLTPGLKVSIRAVCVMRFLVSKRKFKESLRLD
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ2 / Plasmid: pPROEX-HTc, pOKD4 / Production host: Escherichia coli (E. coli) / References: UniProt: O43526
#2: Protein Calmodulin-1 /


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ...Details: MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAKADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Plasmid: pOKD4 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N TROSY-HSQC
121isotropic12D 1H-13C TROSY-HSQC
161isotropic13D HNCA
141isotropic13D HN(CA)CB
171isotropic13D HNCO
1101isotropic13D HN(CA)CO
181isotropic13D HN(CA)HA
191isotropic13D HN(COCA)HA
1111isotropic13D H(CCO)NH
1121isotropic13D HNC(CCO)NH
1131isotropic13D 1H-15N NOESY
1141isotropic13D 1H-13C NOESY
1371isotropic22D 1H-15N TROSY-HSQC
1334isotropic12D 1H-15N TROSY-HSQC
1344isotropic12D 1H-15N semiTROSY-HSQC
1354anisotropic12D 1H-15N TROSY-HSQC
1364anisotropic12D 1H-15N semiTROSY-HSQC
1152isotropic12D 1H-15N TROSY-HSQC
1162isotropic12D 1H-13C TROSY-HSQC
1172isotropic13D HNCA
1192isotropic13D HN(CA)CB
1212isotropic13D HNCO
1222isotropic13D HN(CA)CO
1232isotropic13D HN(CA)HA
1242isotropic13D HN(COCA)HA
1252isotropic13D H(CCO)NH
1262isotropic13D HNC(CCO)NH
1272isotropic13D 1H-15N NOESY
1282isotropic13D 1H-13C NOESY
1382isotropic22D 1H-15N TROSY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 13C; U-100% 15N; U-50% 2H] Kv7.2-hAB, 1 mM [U-100% 13C; U-100% 15N; U-50% 2H] Calmodulin, 120 mM potassium chloride, 20 mM MES, 5 mM CaCl2, 2 uM sodium azide, 200 uM [U-2H] DSS, 95% H2O/5% D2O2H_13C_15N_complex95% H2O/5% D2O
solution2500 uM [U-100% 13C; U-100% 15N] Kv7.2-hAB, 500 uM Calmodulin, 120 mM potassium chloride, 20 mM MES, 5 mM CaCl2, 2 uM sodium azide, 200 uM [U-2H] DSS, 95% H2O/5% D2O13C_15N_Kv7.2-hAB95% H2O/5% D2O
solution4250 uM [U-100% 15N] Kv7.2-hAB, 250 uM [U-100% 15N] Calmodulin, 120 mM potassium chloride, 20 mM MES, 5 mM CaCl2, 2 uM sodium azide, 200 uM [U-2H] DSS, 95% H2O/5% D2O15N_complex95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMKv7.2-hAB[U-100% 13C; U-100% 15N; U-50% 2H]1
1 mMCalmodulin[U-100% 13C; U-100% 15N; U-50% 2H]1
120 mMpotassium chloridenatural abundance1
20 mMMESnatural abundance1
5 mMCaCl2natural abundance1
2 uMsodium azidenatural abundance1
200 uMDSS[U-2H]1
500 uMKv7.2-hAB[U-100% 13C; U-100% 15N]2
500 uMCalmodulinnatural abundance2
120 mMpotassium chloridenatural abundance2
20 mMMESnatural abundance2
5 mMCaCl2natural abundance2
2 uMsodium azidenatural abundance2
200 uMDSS[U-2H]2
250 uMKv7.2-hAB[U-100% 15N]4
250 uMCalmodulin[U-100% 15N]4
120 mMpotassium chloridenatural abundance4
20 mMMESnatural abundance4
5 mMCaCl2natural abundance4
2 uMsodium azidenatural abundance4
200 uMDSS[U-2H]4
Sample conditionsIonic strength: 120 mM / Label: general_conditions / pH: 6 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceIIIBrukerAvanceIII8001
Bruker AvanceIIIBrukerAvanceIII6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospincollection
Sparky3.115Goddardchemical shift assignment
Sparky3.115Goddardpeak picking
Sparky3.115Goddarddata analysis
CcpNmr Analysis2.4CCPNchemical shift assignment
CcpNmr Analysis2.4CCPNdata analysis
NMRPipe8.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA2.3.1Linge, O'Donoghue and Nilgesstructure calculation
ARIA2.3.1Linge, O'Donoghue and Nilgesdata analysis
ARIA2.3.1Linge, O'Donoghue and Nilgesrefinement
PROCHECK / PROCHECK-NMRLaskowski and MacArthurdata analysis
MolProbityRichardsondata analysis
AQUARullmann, Doreleijers and Kapteindata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 10

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