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- PDB-5vms: CryoEM structure of Xenopus KCNQ1 channel -

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Basic information

Entry
Database: PDB / ID: 5vms
TitleCryoEM structure of Xenopus KCNQ1 channel
Components
  • Calmodulin
  • Potassium voltage-gated channel subfamily KQT member 1
KeywordsTRANSPORT PROTEIN / CALCIUM BINDING PROTEIN / KCNQ1-CaM complex / potassium channel / Long QT syndrome
Function / homology
Function and homology information


regulation of gastric acid secretion / membrane repolarization / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / delayed rectifier potassium channel activity / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding ...regulation of gastric acid secretion / membrane repolarization / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / : / establishment of protein localization to mitochondrial membrane / delayed rectifier potassium channel activity / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding / outward rectifier potassium channel activity / CaM pathway / intestinal absorption / 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 / positive regulation of DNA binding / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / positive regulation of peptidyl-threonine phosphorylation / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / presynaptic endocytosis / renal absorption / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / inner ear development / regulation of synaptic vesicle endocytosis / Ion transport by P-type ATPases / positive regulation of protein autophosphorylation / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / voltage-gated potassium channel activity / monoatomic ion channel complex / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / enzyme regulator activity / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / voltage-gated potassium channel complex / phosphatidylinositol-4,5-bisphosphate binding / potassium ion transmembrane transport / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / nitric-oxide synthase regulator activity / FCERI mediated Ca+2 mobilization / response to amphetamine / positive regulation of nitric-oxide synthase activity / Ras activation upon Ca2+ influx through NMDA receptor / cytoplasmic vesicle membrane / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
Similarity search - Function
Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Voltage-dependent channel domain superfamily / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif ...Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Voltage-dependent channel domain superfamily / EF-hand / : / Recoverin; domain 1 / 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. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-3 / Potassium voltage-gated channel subfamily KQT member 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMackinnon, R. / Sun, J.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
American Heart Association17POST32260003 United States
CitationJournal: Cell / Year: 2017
Title: Cryo-EM Structure of a KCNQ1/CaM Complex Reveals Insights into Congenital Long QT Syndrome.
Authors: Ji Sun / Roderick MacKinnon /
Abstract: KCNQ1 is the pore-forming subunit of cardiac slow-delayed rectifier potassium (I) channels. Mutations in the kcnq1 gene are the leading cause of congenital long QT syndrome (LQTS). Here, we present ...KCNQ1 is the pore-forming subunit of cardiac slow-delayed rectifier potassium (I) channels. Mutations in the kcnq1 gene are the leading cause of congenital long QT syndrome (LQTS). Here, we present the cryoelectron microscopy (cryo-EM) structure of a KCNQ1/calmodulin (CaM) complex. The conformation corresponds to an "uncoupled," PIP-free state of KCNQ1, with activated voltage sensors and a closed pore. Unique structural features within the S4-S5 linker permit uncoupling of the voltage sensor from the pore in the absence of PIP. CaM contacts the KCNQ1 voltage sensor through a specific interface involving a residue on CaM that is mutated in a form of inherited LQTS. Using an electrophysiological assay, we find that this mutation on CaM shifts the KCNQ1 voltage-activation curve. This study describes one physiological form of KCNQ1, depolarized voltage sensors with a closed pore in the absence of PIP, and reveals a regulatory interaction between CaM and KCNQ1 that may explain CaM-mediated LQTS.
History
DepositionApr 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_image_scans / em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Other / Category: cell / citation / citation_author
Item: _cell.Z_PDB / _citation.journal_abbrev ..._cell.Z_PDB / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,6365
Polymers79,5162
Non-polymers1203
Water00
1
A: Potassium voltage-gated channel subfamily KQT member 1
B: Calmodulin
hetero molecules

A: Potassium voltage-gated channel subfamily KQT member 1
B: Calmodulin
hetero molecules

A: Potassium voltage-gated channel subfamily KQT member 1
B: Calmodulin
hetero molecules

A: Potassium voltage-gated channel subfamily KQT member 1
B: Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,54520
Polymers318,0648
Non-polymers48112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C4 (4 fold cyclic))

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Components

#1: Protein Potassium voltage-gated channel subfamily KQT member 1 / IKs producing slow voltage-gated potassium channel subunit alpha xKvLQT1 / KQT-like 1 / Voltage- ...IKs producing slow voltage-gated potassium channel subunit alpha xKvLQT1 / KQT-like 1 / Voltage-gated potassium channel subunit Kv7.1 / KCNQ1


Mass: 62663.398 Da / Num. of mol.: 1 / Fragment: UNP residues 67-610
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: kcnq1, kvlqt1 / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: P70057
#2: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Homo sapiens (human) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of Xenopus KCNQ1 and CaM / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293 GnTI- cells
Buffer solutionpH: 7.2
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Chamber temperature: 298 K / Details: 90-100% humidity

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.78 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
EM software
IDNameVersionCategory
13RELION1.33D reconstruction
14FREALIGN9.033D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69415
Details: Entry was refined using space group P4 and cell parameters a=b=c=332.8 and alpha=beta=gamma=90.
Symmetry type: POINT
RefinementResolution: 3.7→122.3 Å / Cor.coef. Fo:Fc: 0.91 / SU B: 40.602 / SU ML: 0.52
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.30701 --
obs0.30701 14320 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 203.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0 Å2-0 Å2
2--0.77 Å2-0 Å2
3----1.54 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0193807
ELECTRON MICROSCOPYr_bond_other_d0.0010.023639
ELECTRON MICROSCOPYr_angle_refined_deg1.2281.9345161
ELECTRON MICROSCOPYr_angle_other_deg0.88238240
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.2835480
ELECTRON MICROSCOPYr_dihedral_angle_2_deg25.24622155
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.41615604
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.2641529
ELECTRON MICROSCOPYr_chiral_restr0.0760.2592
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.024321
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02968
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it4.55420.591932
ELECTRON MICROSCOPYr_mcbond_other4.55320.591931
ELECTRON MICROSCOPYr_mcangle_it7.46630.8882408
ELECTRON MICROSCOPYr_mcangle_other7.46530.892409
ELECTRON MICROSCOPYr_scbond_it5.41421.3571875
ELECTRON MICROSCOPYr_scbond_other5.41321.3591876
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other9.64131.7752754
ELECTRON MICROSCOPYr_long_range_B_refined13.3218348
ELECTRON MICROSCOPYr_long_range_B_other13.3218349
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.7→3.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.524 1063 -
Rfree-0 -
obs--100 %

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