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- EMDB-32334: CryoEM structure of human KChIP2-Kv4.3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32334
TitleCryoEM structure of human KChIP2-Kv4.3 complex
Map data
Sample
  • Complex: Complex of voltage-gated potassium channel Kv4.3 with KChIP2
    • Protein or peptide: Kv channel-interacting protein 2
    • Protein or peptide: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
KeywordsKv channel-interacting protein 2 Potassium voltage-gated channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


ventricular cardiac muscle cell membrane repolarization / ER retention sequence binding / Kv4.3-KChIP1 channel complex / 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 / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / positive regulation of potassium ion export across plasma membrane / clustering of voltage-gated potassium channels ...ventricular cardiac muscle cell membrane repolarization / ER retention sequence binding / Kv4.3-KChIP1 channel complex / 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 / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / positive regulation of potassium ion export across plasma membrane / clustering of voltage-gated potassium 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 / regulation of membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / postsynaptic specialization membrane / regulation of heart contraction / regulation of heart rate by cardiac conduction / action potential / potassium channel activity / detection of calcium ion / regulation of signal transduction / potassium channel regulator activity / muscle contraction / voltage-gated potassium channel complex / potassium ion transmembrane transport / GABA-ergic synapse / protein tetramerization / potassium ion transport / sarcolemma / protein homooligomerization / chemical synaptic transmission / dendritic spine / transmembrane transporter binding / postsynaptic membrane / neuronal cell body / synapse / dendrite / calcium ion binding / protein-containing complex binding / signal transduction / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Potassium channel, voltage dependent, Kv4.3 / 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, Kv4.3 / 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 / 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
A-type potassium channel modulatory protein KCNIP2 / A-type voltage-gated potassium channel KCND3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMa DM / Guo JT
Funding support4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021FZZX001-28
Ministry of Science and Technology (MoST, China)LD21H020001
National Natural Science Foundation of China (NSFC)LR19C050002
National Natural Science Foundation of China (NSFC)LY19H020007
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, 2021-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32334.png

Downloads & links

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Map

FileDownload / File: emd_32334.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 270 pix.
= 273.78 Å		1.01 Å/pix.
x 270 pix.
= 273.78 Å		1.01 Å/pix.
x 270 pix.
= 273.78 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0109
Minimum - Maximum-0.05346814 - 0.09232946
Average (Standard dev.)-0.000031259344 (±0.0024764526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 273.78003 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Complex of voltage-gated potassium channel Kv4.3 with KChIP2

EntireName: Complex of voltage-gated potassium channel Kv4.3 with KChIP2
Components
  • Complex: Complex of voltage-gated potassium channel Kv4.3 with KChIP2
    • Protein or peptide: Kv channel-interacting protein 2
    • Protein or peptide: Isoform 2 of Potassium voltage-gated channel subfamily D member 3

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Supramolecule #1: Complex of voltage-gated potassium channel Kv4.3 with KChIP2

SupramoleculeName: Complex of voltage-gated potassium channel Kv4.3 with KChIP2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Kv channel-interacting protein 2

MacromoleculeName: Kv channel-interacting protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.693582 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRGQGRKESL SDSRDLDGSY DQLTGHPPGP TKKALKQRFL KLLPCCGPQA LPSVSETLAA PASLRPHRPR LLDPDSVDDE FELSTVCHR PEGLEQLQEQ TKFTRKELQV LYRGFKNECP SGIVNEENFK QIYSQFFPQG DSSTYATFLF NAFDTNHDGS V SFEDFVAG ...String:
MRGQGRKESL SDSRDLDGSY DQLTGHPPGP TKKALKQRFL KLLPCCGPQA LPSVSETLAA PASLRPHRPR LLDPDSVDDE FELSTVCHR PEGLEQLQEQ TKFTRKELQV LYRGFKNECP SGIVNEENFK QIYSQFFPQG DSSTYATFLF NAFDTNHDGS V SFEDFVAG LSVILRGTVD DRLNWAFNLY DLNKDGCITK EEMLDIMKSI YDMMGKYTYP ALREEAPREH VESFFQKMDR NK DGVVTIE EFIESCQKDE NIMRSMQLFD NVILEGGSSG GHHHHHHHH

UniProtKB: A-type potassium channel modulatory protein KCNIP2

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Macromolecule #2: Isoform 2 of Potassium voltage-gated channel subfamily D member 3

MacromoleculeName: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.472781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAGVAAWLP FARAAAIGWM PVANCPMPLA PADKNKRQDE LIVLNVSGRR FQTWRTTLER YPDTLLGSTE KEFFFNEDTK EYFFDRDPE VFRCVLNFYR TGKLHYPRYE CISAYDDELA FYGILPEIIG DCCYEEYKDR KRENAERLMD DNDSENNQES M PSLSFRQT ...String:
MAAGVAAWLP FARAAAIGWM PVANCPMPLA PADKNKRQDE LIVLNVSGRR FQTWRTTLER YPDTLLGSTE KEFFFNEDTK EYFFDRDPE VFRCVLNFYR TGKLHYPRYE CISAYDDELA FYGILPEIIG DCCYEEYKDR KRENAERLMD DNDSENNQES M PSLSFRQT MWRAFENPHT STLALVFYYV TGFFIAVSVI TNVVETVPCG TVPGSKELPC GERYSVAFFC LDTACVMIFT VE YLLRLFA APSRYRFIRS VMSIIDVVAI MPYYIGLVMT NNEDVSGAFV TLRVFRVFRI FKFSRHSQGL RILGYTLKSC ASE LGFLLF SLTMAIIIFA TVMFYAEKGS SASKFTSIPA SFWYTIVTMT TLGYGDMVPK TIAGKIFGSI CSLSGVLVIA LPVP VIVSN FSRIYHQNQR ADKRRAQKKA RLARIRVAKT GSSNAYLHSK RNGLLNEALE LTGTPEEEHM GKTTSLIESQ HHHLL HCLE KTTNHEFIDE QMFEQNCMES SMQNYPSTRS PSLSSHPGLT TTCCSRRSKK TTHLPNSNLP ATRLRSMQEL STIHIQ GSE QPSLTTSRSS LNLKADDGLR PNCKTSQITT AIISIPTPPA LTPEGESRPP PASPGPNTNI PSIASNVVKV SAL

UniProtKB: A-type voltage-gated potassium channel KCND3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 240437
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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