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Yorodumi- EMDB-31018: CryoEM structure of human Kv4.2-DPP6S-KChIP1 complex, extracellul... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31018 | |||||||||
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Title | CryoEM structure of human Kv4.2-DPP6S-KChIP1 complex, extracellular region | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information regulation of potassium ion transmembrane transport / potassium channel regulator activity / voltage-gated potassium channel complex / serine-type peptidase activity / protein localization to plasma membrane / proteolysis / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Kise Y / Nureki O | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31018.map.gz | 14.7 MB | EMDB map data format | |
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Header (meta data) | emd-31018-v30.xml emd-31018.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31018_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_31018.png | 42.3 KB | ||
Masks | emd_31018_msk_1.map | 101 MB | Mask map | |
Others | emd_31018_half_map_1.map.gz emd_31018_half_map_2.map.gz | 77.5 MB 77.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31018 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31018 | HTTPS FTP |
-Validation report
Summary document | emd_31018_validation.pdf.gz | 625.2 KB | Display | EMDB validaton report |
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Full document | emd_31018_full_validation.pdf.gz | 624.8 KB | Display | |
Data in XML | emd_31018_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | emd_31018_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31018 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31018 | HTTPS FTP |
-Related structure data
Related structure data | 7e8gMC 7e7zC 7e83C 7e84C 7e87C 7e89C 7e8bC 7e8eC 7e8hC 7f0jC 7f3fC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31018.map.gz / Format: CCP4 / Size: 101 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.00268 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_31018_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31018_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31018_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human Kv4.2-DPP6S-KChIP1 complex
Entire | Name: human Kv4.2-DPP6S-KChIP1 complex |
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Components |
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-Supramolecule #1: human Kv4.2-DPP6S-KChIP1 complex
Supramolecule | Name: human Kv4.2-DPP6S-KChIP1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Dipeptidyl aminopeptidase-like protein 6
Macromolecule | Name: Dipeptidyl aminopeptidase-like protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 83.476094 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EDNSLSQKKK VTVEDLFSED FKIHDPEAKW ISDTEFIYRE QKGTVRLWNV ETNTSTVLIE GKKIESLRAI RYEISPDREY ALFSYNVEP IYQHSYTGYY VLSKIPHGDP QSLDPPEVSN AKLQYAGWGP KGQQLIFIFE NNIYYCAHVG KQAIRVVSTG K EGVIYNGL ...String: EDNSLSQKKK VTVEDLFSED FKIHDPEAKW ISDTEFIYRE QKGTVRLWNV ETNTSTVLIE GKKIESLRAI RYEISPDREY ALFSYNVEP IYQHSYTGYY VLSKIPHGDP QSLDPPEVSN AKLQYAGWGP KGQQLIFIFE NNIYYCAHVG KQAIRVVSTG K EGVIYNGL SDWLYEEEIL KTHIAHWWSP DGTRLAYAAI NDSRVPIMEL PTYTGSIYPT VKPYHYPKAG SENPSISLHV IG LNGPTHD LEMMPPDDPR MREYYITMVK WATSTKVAVT WLNRAQNVSI LTLCDATTGV CTKKHEDESE AWLHRQNEEP VFS KDGRKF FFIRAIPQGG RGKFYHITVS SSQPNSSNDN IQSITSGDWD VTKILAYDEK GNKIYFLSTE DLPRRRQLYS ANTV GNFNR QCLSCDLVEN CTYFSASFSH SMDFFLLKCE GPGVPMVTVH NTTDKKKMFD LETNEHVKKA INDRQMPKVE YRDIE IDDY NLPMQILKPA TFTDTTHYPL LLVVDGTPGS QSVAEKFEVS WETVMVSSHG AVVVKCDGRG SGFQGTKLLH EVRRRL GLL EEKDQMEAVR TMLKEQYIDR TRVAVFGKDY GGYLSTYILP AKGENQGQTF TCGSALSPIT DFKLYASAFS ERYLGLH GL DNRAYEMTKV AHRVSALEEQ QFLIIHPTAD EKIHFQHTAE LITQLIRGKA NYSLQIYPDE SHYFTSSSLK QHLYRSII N FFVECFRI |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |