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- PDB-7w6n: CryoEM structure of human KChIP1-Kv4.3 complex -

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Basic information

Entry
Database: PDB / ID: 7w6n
TitleCryoEM structure of human KChIP1-Kv4.3 complex
Components
  • Isoform 2 of Potassium voltage-gated channel subfamily D member 3
  • Kv channel-interacting protein 1
KeywordsMEMBRANE PROTEIN / Kv channel-interacting protein 1 Potassium voltage-gated channel
Function / homology
Function and homology information


ventricular cardiac muscle cell membrane repolarization / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / postsynaptic specialization membrane ...ventricular cardiac muscle cell membrane repolarization / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / membrane repolarization during ventricular cardiac muscle cell action potential / membrane repolarization during cardiac muscle cell action potential / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / postsynaptic specialization membrane / voltage-gated potassium channel activity / potassium channel activity / regulation of heart rate by cardiac conduction / GABA-ergic synapse / potassium channel regulator activity / voltage-gated potassium channel complex / potassium ion transport / protein homooligomerization / cytoplasmic side of plasma membrane / sarcolemma / postsynaptic membrane / transmembrane transporter binding / dendritic spine / neuronal cell body / calcium ion binding / dendrite / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, voltage dependent, Kv4.3 / Potassium channel, voltage dependent, Kv4 / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv4, C-terminal / Shal-type voltage-gated potassium channels, N-terminal / Domain of unknown function (DUF3399) / Recoverin family / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain ...Potassium channel, voltage dependent, Kv4.3 / Potassium channel, voltage dependent, Kv4 / Shal-type voltage-gated potassium channels, N-terminal / Potassium channel, voltage dependent, Kv4, C-terminal / Shal-type voltage-gated potassium channels, N-terminal / Domain of unknown function (DUF3399) / Recoverin family / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / EF-hand domain pair / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Voltage-dependent channel domain superfamily / SKP1/BTB/POZ 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. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Kv channel-interacting protein 1 / Potassium voltage-gated channel subfamily D member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMa, D.M. / Guo, J.T.
Funding support China, 4items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021FZZX001-28 China
Ministry of Science and Technology (MoST, China)LD21H020001 China
National Natural Science Foundation of China (NSFC)LR19C050002 China
National Natural Science Foundation of China (NSFC)LY19H020007 China
CitationJournal: Cell Res / Year: 2022
Title: Structural basis for the gating modulation of Kv4.3 by auxiliary subunits.
Authors: Demin Ma / Cheng Zhao / Xiaochen Wang / Xiaoxiao Li / Yi Zha / Yan Zhang / Guosheng Fu / Ping Liang / Jiangtao Guo / Dongwu Lai /
History
DepositionDec 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kv channel-interacting protein 1
B: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
C: Kv channel-interacting protein 1
D: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
E: Kv channel-interacting protein 1
F: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
G: Kv channel-interacting protein 1
H: Isoform 2 of Potassium voltage-gated channel subfamily D member 3


Theoretical massNumber of molelcules
Total (without water)393,6338
Polymers393,6338
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Kv channel-interacting protein 1 / KChIP1 / A-type potassium channel modulatory protein 1 / Potassium channel-interacting protein 1 / ...KChIP1 / A-type potassium channel modulatory protein 1 / Potassium channel-interacting protein 1 / Vesicle APC-binding protein


Mass: 26935.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNIP1, KCHIP1, VABP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NZI2
#2: Protein
Isoform 2 of Potassium voltage-gated channel subfamily D member 3 / Voltage-gated potassium channel subunit Kv4.3


Mass: 71472.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCND3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9UK17

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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 voltage-gated potassium channel Kv4.3 with KChIP1
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 8 sec. / Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81213 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01120200
ELECTRON MICROSCOPYf_angle_d0.84627328
ELECTRON MICROSCOPYf_dihedral_angle_d8.80411980
ELECTRON MICROSCOPYf_chiral_restr0.0513012
ELECTRON MICROSCOPYf_plane_restr0.0063468

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