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- EMDB-32335: CryoEM structure of human KChIP1-Kv4.3-DPP6 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32335
TitleCryoEM structure of human KChIP1-Kv4.3-DPP6 complex
Map data
Sample
  • Complex: Complex of voltage-gated potassium channel Kv4.3 with auxiliary subunits KChIP1 and DPP6
    • Protein or peptide: Kv channel-interacting protein 1
    • Protein or peptide: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
    • Protein or peptide: Dipeptidyl aminopeptidase-like protein 6
KeywordsKv channel-interacting protein 1 Potassium voltage-gated channel Dipeptidyl aminopeptidase-like protein 6 / MEMBRANE PROTEIN
Function / homology
Function and homology information


ventricular cardiac muscle cell membrane repolarization / Kv4.3-KChIP1 channel complex / 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 ...ventricular cardiac muscle cell membrane repolarization / Kv4.3-KChIP1 channel complex / 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 / regulation of heart contraction / action potential / regulation of heart rate by cardiac conduction / voltage-gated potassium channel activity / potassium channel activity / potassium channel regulator activity / voltage-gated potassium channel complex / GABA-ergic synapse / muscle contraction / potassium ion transmembrane transport / serine-type peptidase activity / protein tetramerization / potassium ion transport / protein homooligomerization / sarcolemma / cytoplasmic side of plasma membrane / chemical synaptic transmission / postsynaptic membrane / transmembrane transporter binding / dendritic spine / neuronal cell body / dendrite / calcium ion binding / synapse / proteolysis / metal ion 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 / : / 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 KCND3
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsMa DM / Guo JT
Funding support China, 4 items
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, 2021-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32335.png

Downloads & links

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Map

FileDownload / File: emd_32335.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: 0.0956
Minimum - Maximum-0.45715824 - 1.0799412
Average (Standard dev.)-0.0046180715 (±0.058762778)
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 auxiliary s...

EntireName: Complex of voltage-gated potassium channel Kv4.3 with auxiliary subunits KChIP1 and DPP6
Components
  • Complex: Complex of voltage-gated potassium channel Kv4.3 with auxiliary subunits KChIP1 and DPP6
    • Protein or peptide: Kv channel-interacting protein 1
    • Protein or peptide: Isoform 2 of Potassium voltage-gated channel subfamily D member 3
    • Protein or peptide: Dipeptidyl aminopeptidase-like protein 6

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

SupramoleculeName: Complex of voltage-gated potassium channel Kv4.3 with auxiliary subunits KChIP1 and DPP6
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 1

MacromoleculeName: Kv channel-interacting protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.935469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SMGAVMGTFS SLQTKQRRPS KDIAWWYYQY QRDKIEDELE MTMVCHRPEG LEQLEAQTNF TKRELQVLYR GFKNECPSGV VNEDTFKQI YAQFFPHGDA STYAHYLFNA FDTTQTGSVK FEDFVTALSI LLRGTVHEKL RWTFNLYDIN KDGYINKEEM M DIVKAIYD ...String:
SMGAVMGTFS SLQTKQRRPS KDIAWWYYQY QRDKIEDELE MTMVCHRPEG LEQLEAQTNF TKRELQVLYR GFKNECPSGV VNEDTFKQI YAQFFPHGDA STYAHYLFNA FDTTQTGSVK FEDFVTALSI LLRGTVHEKL RWTFNLYDIN KDGYINKEEM M DIVKAIYD MMGKYTYPVL KEDTPRQHVD VFFQKMDKNK DGIVTLDEFL ESCQEDDNIM RSLQLFQNVM

UniProtKB: A-type potassium channel modulatory protein KCNIP1

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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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Macromolecule #3: Dipeptidyl aminopeptidase-like protein 6

MacromoleculeName: Dipeptidyl aminopeptidase-like protein 6 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 98.874242 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASLYQRFTG KINTSRSFPA PPEASRLLGG QGPEEDAGPK PLGPQAQAVA PRERGGAGGR PRFQYQARSD CDEEDELVGS NPPQRNWKG IAIALLVILV ICSLIVTSVI LLTPAEDTSL SQKKKVTVED LFSEDFKIHD PEAKWISNKE FIYRERKGSV I LRNVETNN ...String:
MASLYQRFTG KINTSRSFPA PPEASRLLGG QGPEEDAGPK PLGPQAQAVA PRERGGAGGR PRFQYQARSD CDEEDELVGS NPPQRNWKG IAIALLVILV ICSLIVTSVI LLTPAEDTSL SQKKKVTVED LFSEDFKIHD PEAKWISNKE FIYRERKGSV I LRNVETNN STVLIEGKKI ESLRAIRYEI SPDKEYVLFS YNVEPVYQHS HTGYYVLSKI PHGDPQSLDP PEVSNAKLQY AG WGPKGQQ LIFIFENNIY YCAHVGKQAI RVVSTGKEGV IYNGLSDWLY EEEILKSHIA HWWSPDGTRL AYATINDSRV PLM ELPTYT GSVYPTVKPY HYPKAGSENP SISLHVIGLN GPTHDLEMMP PDDPRMREYY ITMVKWATST KVAVTWLNRA QNVS ILTLC DATTGVCTKK HEDESEAWLH RQNEEPVFSK DGRKFFFVRA IPQGGRGKFY HITVSSSQPN SSNDNIQSIT SGDWD VTKI LSYDEKRNKI YFLSTEDLPR RRHLYSANTV DDFNRQCLSC DLVENCTYVS ASFSHNMDFF LLKCEGPGVP TVTVHN TTD KRRMFDLEAN EEVQKAINDR QMPKIEYRKI EVEDYSLPMQ ILKPATFTDT AHYPLLLVVD GTPGSQSVTE RFEVTWE TV LVSSHGAVVV KCDGRGSGFQ GTKLLQEVRR RLGFLEEKDQ MEAVRTMLKE QYIDKTRVAV FGKDYGGYLS TYILPAKG E NQGQTFTCGS ALSPITDFKL YASAFSERYL GLHGLDNRAY EMTKLAHRVS ALEDQQFLII HATADEKIHF QHTAELITQ LIKGKANYSL QIYPDESHYF HSVALKQHLS RSIIGFFVEC FRVQDKLPTA TAKEEEEEDL EGGSSDYKDD DDK

UniProtKB: A-type potassium channel modulatory protein DPP6

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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 K3 (6k x 4k) / Average exposure time: 2.8 sec. / Average electron dose: 65.0 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 / Nominal defocus max: -1.3 µm / Nominal defocus min: -1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7w6t

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 263176
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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