[English] 日本語
Yorodumi
- PDB-5k7l: Single particle cryo-EM structure of the voltage-gated K+ channel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k7l
TitleSingle particle cryo-EM structure of the voltage-gated K+ channel Eag1 bound to the channel inhibitor calmodulin
Components
  • Calmodulin
  • Potassium voltage-gated channel subfamily H member 1
KeywordsMETAL TRANSPORT/CALCIUM BINDING PROTEIN / Voltage-gated potassium channel / calmodulin / Cryoelectron microscopy / Eag1 / METAL TRANSPORT-CALCIUM BINDING PROTEIN complex
Function / homology
Function and homology information


Voltage gated Potassium channels / potassium channel complex / regulation of presynaptic cytosolic calcium ion concentration / delayed rectifier potassium channel activity / : / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / parallel fiber to Purkinje cell synapse / CaM pathway ...Voltage gated Potassium channels / potassium channel complex / regulation of presynaptic cytosolic calcium ion concentration / delayed rectifier potassium channel activity / : / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / parallel fiber to Purkinje cell synapse / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / nuclear inner membrane / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / regulation of synaptic vesicle endocytosis / phosphatidylinositol bisphosphate binding / 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 / regulation of synaptic vesicle exocytosis / 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 / response to corticosterone / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / startle response / 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 / 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 / adenylate cyclase binding / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / axolemma / 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 / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / enzyme regulator activity / voltage-gated potassium channel complex / phosphatidylinositol 3-kinase binding / 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 / response to amphetamine / calcium channel complex / activation of adenylate cyclase activity / substantia nigra development / cellular response to calcium ion / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of membrane potential / monoatomic ion transmembrane transport / regulation of heart rate / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / 14-3-3 protein binding / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers
Similarity search - Function
Potassium channel, voltage-dependent, EAG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...Potassium channel, voltage-dependent, EAG / Potassium channel, voltage-dependent, EAG/ELK/ERG / PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / PAS repeat profile. / PAS domain / RmlC-like jelly roll fold / PAS domain superfamily / 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
CHOLESTEROL HEMISUCCINATE / Calmodulin-1 / Calmodulin-3 / Potassium voltage-gated channel subfamily H member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsWhicher, J.R. / MacKinnon, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM43949 United States
Howard Hughes Medical Institute (HHMI) United States
Damon Runyon Cancer Research FoundationDRG-2212-15 United States
CitationJournal: Science / Year: 2016
Title: Structure of the voltage-gated K⁺ channel Eag1 reveals an alternative voltage sensing mechanism.
Authors: Jonathan R Whicher / Roderick MacKinnon /
Abstract: Voltage-gated potassium (K(v)) channels are gated by the movement of the transmembrane voltage sensor, which is coupled, through the helical S4-S5 linker, to the potassium pore. We determined the ...Voltage-gated potassium (K(v)) channels are gated by the movement of the transmembrane voltage sensor, which is coupled, through the helical S4-S5 linker, to the potassium pore. We determined the single-particle cryo-electron microscopy structure of mammalian K(v)10.1, or Eag1, bound to the channel inhibitor calmodulin, at 3.78 angstrom resolution. Unlike previous K(v) structures, the S4-S5 linker of Eag1 is a five-residue loop and the transmembrane segments are not domain swapped, which suggest an alternative mechanism of voltage-dependent gating. Additionally, the structure and position of the S4-S5 linker allow calmodulin to bind to the intracellular domains and to close the potassium pore, independent of voltage-sensor position. The structure reveals an alternative gating mechanism for K(v) channels and provides a template to further understand the gating properties of Eag1 and related channels.
History
DepositionMay 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Database references
Category: citation / em_image_scans ...citation / em_image_scans / em_software / pdbx_audit_support
Item: _citation.journal_id_CSD / _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Movie
  • Biological unit as complete point assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8215
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)114,9204
Polymers114,2122
Non-polymers7082
Water0
1
A: Potassium voltage-gated channel subfamily H member 1
B: Calmodulin
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)459,68116
Polymers456,8498
Non-polymers2,8328
Water0
TypeNameSymmetry operationNumber
point symmetry operation4
2


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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))

-
Components

#1: Protein Potassium voltage-gated channel subfamily H member 1 / Voltage-gated potassium channel Eag1 / Ether-a-go-go potassium channel 1 / r-eag / Voltage-gated ...Voltage-gated potassium channel Eag1 / Ether-a-go-go potassium channel 1 / r-eag / Voltage-gated potassium channel subunit Kv10.1


Mass: 97359.766 Da / Num. of mol.: 1 / Fragment: UNP residues 1-773, 888-962
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kcnh1, Eag / Plasmid: pEG BacMam / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q63472
#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
Plasmid: pEG BacMam / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Voltage-gated K+ channel Eag1 bound to the channel inhibitor calmodulinORGANELLE OR CELLULAR COMPONENT#1-#20MULTIPLE SOURCES
2Voltage-gated potassium channel Eag1ORGANELLE OR CELLULAR COMPONENT#11RECOMBINANT
3CalmodulinORGANELLE OR CELLULAR COMPONENT#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.45 MDaNO
220.38 MDaNO
330.017 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDCellular location
12Rattus norvegicus (Norway rat)10116Cell membrane
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
12Homo sapiens (human)9606HEK293 GnTI-pEG BacMam
23Homo sapiens (human)9606HEK293 GnTI-pEG BacMam
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2300 mMpotassium chlorideKCl1
35 mMcalcium chlorideCaCl21
45 mMDTT1
51 mMDodecyl Maltopyranoside1
60.2 mMCholesteryl hemisuccinate1
70.05 mg/mLPC:PE:PS (3:1:1)1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 86 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV)

-
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 FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 1657

-
Processing

SoftwareName: REFMAC / Version: 5.8.0088 / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
4CTFFIND44CTF correction
7Cootmodel fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11FREALIGNfinal Euler assignment
13FREALIGN3D reconstruction
14REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 240000
Details: Particles were auto-picked and manually inspected in RELION.
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145000
Details: 2D classification, 3D classification, and refinement were performed in RELION. Final map generation was performed in FREALIGN.
Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: RECIPROCAL
RefinementResolution: 3.78→165 Å / Cor.coef. Fo:Fc: 0.979 / SU B: 61.954 / SU ML: 0.725 / ESU R: 0.687
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.27167 --
obs0.27167 38517 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: 301.016 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.39 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0196322
ELECTRON MICROSCOPYr_bond_other_d0.0010.025630
ELECTRON MICROSCOPYr_angle_refined_deg1.1881.9468653
ELECTRON MICROSCOPYr_angle_other_deg0.909312766
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.7655839
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.6823.517236
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.40815841
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.0171524
ELECTRON MICROSCOPYr_chiral_restr0.0710.21024
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.027343
ELECTRON MICROSCOPYr_gen_planes_other0.0010.021496
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_it10.27233.1413368
ELECTRON MICROSCOPYr_mcbond_other10.26433.1413367
ELECTRON MICROSCOPYr_mcangle_it16.9549.7094203
ELECTRON MICROSCOPYr_mcangle_other16.94949.714204
ELECTRON MICROSCOPYr_scbond_it19.89532.2042954
ELECTRON MICROSCOPYr_scbond_other19.89132.2052955
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other26.61448.3494451
ELECTRON MICROSCOPYr_long_range_B_refined29.63911517
ELECTRON MICROSCOPYr_long_range_B_other29.63811518
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.78→3.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.689 2822 -
Rfree-0 -
obs--100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more