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- PDB-7ukh: Human Kv4.2-KChIP2-DPP6 channel complex in an open state, intrace... -

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Basic information

Entry
Database: PDB / ID: 7ukh
TitleHuman Kv4.2-KChIP2-DPP6 channel complex in an open state, intracellular region
Components
  • Isoform 2 of Kv channel-interacting protein 2
  • Potassium voltage-gated channel subfamily D member 2
KeywordsMEMBRANE PROTEIN / potassium channel complex
Function / homology
Function and homology information


ER retention sequence binding / regulation of potassium ion export across plasma membrane / Kv4.2-KChIP2 channel complex / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / positive regulation of potassium ion export across plasma membrane / clustering of voltage-gated potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / membrane repolarization during cardiac muscle cell action potential / membrane repolarization ...ER retention sequence binding / regulation of potassium ion export across plasma membrane / Kv4.2-KChIP2 channel complex / A-type (transient outward) potassium channel activity / Phase 1 - inactivation of fast Na+ channels / positive regulation of potassium ion export across plasma membrane / clustering of voltage-gated potassium channels / voltage-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / membrane repolarization during cardiac muscle cell action potential / membrane repolarization / regulation of membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / anchoring junction / neuronal cell body membrane / postsynaptic specialization membrane / regulation of heart contraction / locomotor rhythm / action potential / plasma membrane raft / voltage-gated potassium channel activity / potassium channel activity / detection of calcium ion / regulation of signal transduction / potassium channel regulator activity / neuronal action potential / muscle contraction / voltage-gated potassium channel complex / sensory perception of pain / potassium ion transmembrane transport / GABA-ergic synapse / potassium ion transport / protein homooligomerization / chemical synaptic transmission / cellular response to hypoxia / dendritic spine / perikaryon / transmembrane transporter binding / postsynaptic membrane / neuronal cell body / synapse / dendrite / calcium ion binding / protein-containing complex binding / glutamatergic synapse / signal transduction / metal ion binding / identical protein 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 / Voltage-gated potassium channel / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / EF-hand domain pair / Broad-Complex, Tramtrack and Bric a brac / Voltage-dependent channel domain superfamily / BTB/POZ domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
A-type potassium channel modulatory protein KCNIP2 / A-type voltage-gated potassium channel KCND2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsZhao, H. / Dai, Y. / Lee, C.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143282 United States
CitationJournal: Mol Cell / Year: 2022
Title: Activation and closed-state inactivation mechanisms of the human voltage-gated K4 channel complexes.
Authors: Wenlei Ye / Hongtu Zhao / Yaxin Dai / Yingdi Wang / Yu-Hua Lo / Lily Yeh Jan / Chia-Hsueh Lee /
Abstract: The voltage-gated ion channel activity depends on both activation (transition from the resting state to the open state) and inactivation. Inactivation is a self-restraint mechanism to limit ion ...The voltage-gated ion channel activity depends on both activation (transition from the resting state to the open state) and inactivation. Inactivation is a self-restraint mechanism to limit ion conduction and is as crucial to membrane excitability as activation. Inactivation can occur when the channel is open or closed. Although open-state inactivation is well understood, the molecular basis of closed-state inactivation has remained elusive. We report cryo-EM structures of human K4.2 channel complexes in inactivated, open, and closed states. Closed-state inactivation of K4 involves an unprecedented symmetry breakdown for pore closure by only two of the four S4-S5 linkers, distinct from known mechanisms of open-state inactivation. We further capture K4 in a putative resting state, revealing how voltage sensor movements control the pore. Moreover, our structures provide insights regarding channel modulation by KChIP2 and DPP6 auxiliary subunits. Our findings elucidate mechanisms of closed-state inactivation and voltage-dependent activation of the K4 channel.
History
DepositionApr 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily D member 2
B: Potassium voltage-gated channel subfamily D member 2
C: Potassium voltage-gated channel subfamily D member 2
D: Potassium voltage-gated channel subfamily D member 2
I: Isoform 2 of Kv channel-interacting protein 2
J: Isoform 2 of Kv channel-interacting protein 2
K: Isoform 2 of Kv channel-interacting protein 2
L: Isoform 2 of Kv channel-interacting protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,84224
Polymers352,0998
Non-polymers74316
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Potassium voltage-gated channel subfamily D member 2 / Voltage-gated potassium channel subunit Kv4.2


Mass: 59049.332 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
#2: Protein
Isoform 2 of Kv channel-interacting protein 2 / KChIP2 / A-type potassium channel modulatory protein 2 / Cardiac voltage-gated potassium channel ...KChIP2 / A-type potassium channel modulatory protein 2 / Cardiac voltage-gated potassium channel modulatory subunit / Potassium channel-interacting protein 2


Mass: 28975.486 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNIP2, KCHIP2 / Production host: Homo sapiens (human) / References: UniProt: Q9NS61
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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-KChIP2-DPP6 channel complex in an open state, intracellular region
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 85.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 278343 / Symmetry type: POINT

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