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- PDB-7e8e: CryoEM structure of human Kv4.2-DPP6S-KChIP1 complex, transmembra... -

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Basic information

Entry
Database: PDB / ID: 7e8e
TitleCryoEM structure of human Kv4.2-DPP6S-KChIP1 complex, transmembrane and intracellular region
Components
  • (Dipeptidyl aminopeptidase-like protein 6) x 2
  • (Kv channel-interacting protein 1) x 2
  • Potassium voltage-gated channel subfamily D member 2
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Kv4.3-KChIP1 channel complex / Kv4.2-KChIP2 channel complex / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / anchoring junction ...Kv4.3-KChIP1 channel complex / Kv4.2-KChIP2 channel complex / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / potassium ion export across plasma membrane / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / anchoring junction / postsynaptic specialization membrane / regulation of heart contraction / neuronal cell body membrane / plasma membrane raft / locomotor rhythm / action potential / voltage-gated potassium channel activity / potassium channel activity / neuronal action potential / potassium channel regulator activity / voltage-gated potassium channel complex / GABA-ergic synapse / muscle contraction / sensory perception of pain / potassium ion transmembrane transport / serine-type peptidase activity / protein localization to plasma membrane / protein homooligomerization / cytoplasmic side of plasma membrane / cellular response to hypoxia / chemical synaptic transmission / perikaryon / postsynaptic membrane / transmembrane transporter binding / dendritic spine / neuronal cell body / glutamatergic synapse / calcium ion binding / dendrite / synapse / proteolysis / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, voltage dependent, Kv4.2 / Potassium channel, voltage dependent, Kv4 / Potassium channel, voltage dependent, Kv4, C-terminal / Domain of unknown function (DUF3399) / Shal-type voltage-gated potassium channels, N-terminal / Shal-type voltage-gated potassium channels, N-terminal / Recoverin family / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain ...Potassium channel, voltage dependent, Kv4.2 / Potassium channel, voltage dependent, Kv4 / Potassium channel, voltage dependent, Kv4, C-terminal / Domain of unknown function (DUF3399) / Shal-type voltage-gated potassium channels, N-terminal / Shal-type voltage-gated potassium channels, N-terminal / Recoverin family / Potassium channel, voltage dependent, Kv / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / EF-hand domain pair / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
A-type potassium channel modulatory protein DPP6 / A-type potassium channel modulatory protein KCNIP1 / A-type voltage-gated potassium channel KCND2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsKise, Y. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nature / Year: 2021
Title: Structural basis of gating modulation of Kv4 channel complexes.
Authors: Yoshiaki Kise / Go Kasuya / Hiroyuki H Okamoto / Daichi Yamanouchi / Kan Kobayashi / Tsukasa Kusakizako / Tomohiro Nishizawa / Koichi Nakajo / Osamu Nureki /
Abstract: Modulation of voltage-gated potassium (Kv) channels by auxiliary subunits is central to the physiological function of channels in the brain and heart. Native Kv4 tetrameric channels form ...Modulation of voltage-gated potassium (Kv) channels by auxiliary subunits is central to the physiological function of channels in the brain and heart. Native Kv4 tetrameric channels form macromolecular ternary complexes with two auxiliary β-subunits-intracellular Kv channel-interacting proteins (KChIPs) and transmembrane dipeptidyl peptidase-related proteins (DPPs)-to evoke rapidly activating and inactivating A-type currents, which prevent the backpropagation of action potentials. However, the modulatory mechanisms of Kv4 channel complexes remain largely unknown. Here we report cryo-electron microscopy structures of the Kv4.2-DPP6S-KChIP1 dodecamer complex, the Kv4.2-KChIP1 and Kv4.2-DPP6S octamer complexes, and Kv4.2 alone. The structure of the Kv4.2-KChIP1 complex reveals that the intracellular N terminus of Kv4.2 interacts with its C terminus that extends from the S6 gating helix of the neighbouring Kv4.2 subunit. KChIP1 captures both the N and the C terminus of Kv4.2. In consequence, KChIP1 would prevent N-type inactivation and stabilize the S6 conformation to modulate gating of the S6 helices within the tetramer. By contrast, unlike the reported auxiliary subunits of voltage-gated channel complexes, DPP6S interacts with the S1 and S2 helices of the Kv4.2 voltage-sensing domain, which suggests that DPP6S stabilizes the conformation of the S1-S2 helices. DPP6S may therefore accelerate the voltage-dependent movement of the S4 helices. KChIP1 and DPP6S do not directly interact with each other in the Kv4.2-KChIP1-DPP6S ternary complex. Thus, our data suggest that two distinct modes of modulation contribute in an additive manner to evoke A-type currents from the native Kv4 macromolecular complex.
History
DepositionMar 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
G: Kv channel-interacting protein 1
C: Potassium voltage-gated channel subfamily D member 2
K: Dipeptidyl aminopeptidase-like protein 6
H: Kv channel-interacting protein 1
D: Potassium voltage-gated channel subfamily D member 2
L: Dipeptidyl aminopeptidase-like protein 6
E: Kv channel-interacting protein 1
A: Potassium voltage-gated channel subfamily D member 2
I: Dipeptidyl aminopeptidase-like protein 6
F: Kv channel-interacting protein 1
B: Potassium voltage-gated channel subfamily D member 2
J: Dipeptidyl aminopeptidase-like protein 6


Theoretical massNumber of molelcules
Total (without water)319,50512
Polymers319,50512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area54510 Å2
ΔGint-443 kcal/mol
Surface area128100 Å2

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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: 21242.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNIP1, KCHIP1, VABP / Production host: Homo sapiens (human) / References: UniProt: Q9NZI2
#2: Protein
Potassium voltage-gated channel subfamily D member 2 / Voltage-gated potassium channel subunit Kv4.2


Mass: 55755.738 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCND2, KIAA1044 / Production host: Homo sapiens (human) / References: UniProt: Q9NZV8
#3: Protein/peptide Dipeptidyl aminopeptidase-like protein 6 / DPPX / Dipeptidyl aminopeptidase-related protein / Dipeptidyl peptidase 6 / Dipeptidyl peptidase IV- ...DPPX / Dipeptidyl aminopeptidase-related protein / Dipeptidyl peptidase 6 / Dipeptidyl peptidase IV-like protein / Dipeptidyl peptidase VI / DPP VI


Mass: 3032.829 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP6 / Production host: Homo sapiens (human) / References: UniProt: P42658
#4: 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: 21145.826 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNIP1, KCHIP1, VABP / Production host: Homo sapiens (human) / References: UniProt: Q9NZI2
#5: Protein/peptide Dipeptidyl aminopeptidase-like protein 6 / DPPX / Dipeptidyl aminopeptidase-related protein / Dipeptidyl peptidase 6 / Dipeptidyl peptidase IV- ...DPPX / Dipeptidyl aminopeptidase-related protein / Dipeptidyl peptidase 6 / Dipeptidyl peptidase IV-like protein / Dipeptidyl peptidase VI / DPP VI


Mass: 2819.595 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP6 / Production host: Homo sapiens (human) / References: UniProt: P42658

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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: human Kv4.2-DPP6S-KChIP1 complex / Type: CELL / Entity ID: all / Source: MULTIPLE SOURCES
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
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139524 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421878
ELECTRON MICROSCOPYf_angle_d0.6629606
ELECTRON MICROSCOPYf_dihedral_angle_d4.5982922
ELECTRON MICROSCOPYf_chiral_restr0.0443296
ELECTRON MICROSCOPYf_plane_restr0.0053766

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