+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-31013 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of human Kv4.2-DPP6S complex | |||||||||
![]() | map E | |||||||||
![]() |
| |||||||||
Function / homology | ![]() 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 / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / postsynaptic specialization membrane / anchoring junction / action potential ...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 / membrane repolarization / Voltage gated Potassium channels / regulation of potassium ion transmembrane transport / postsynaptic specialization membrane / anchoring junction / action potential / regulation of heart contraction / neuronal cell body membrane / voltage-gated potassium channel activity / plasma membrane raft / locomotor rhythm / GABA-ergic synapse / potassium channel regulator activity / neuronal action potential / potassium ion transmembrane transport / voltage-gated potassium channel complex / sensory perception of pain / serine-type peptidase activity / muscle contraction / protein localization to plasma membrane / protein homooligomerization / cellular response to hypoxia / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / neuronal cell body / glutamatergic synapse / proteolysis / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Kise Y / Nureki O | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 20 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16.5 KB 16.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11.8 KB | Display | ![]() |
Images | ![]() | 74 KB | ||
Masks | ![]() | 139.6 MB | ![]() | |
Others | ![]() ![]() | 108.1 MB 108.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 648.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 648.2 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7e8bMC ![]() 7e7zC ![]() 7e83C ![]() 7e84C ![]() 7e87C ![]() 7e89C ![]() 7e8eC ![]() 7e8gC ![]() 7e8hC ![]() 7f0jC ![]() 7f3fC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | map E | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_31013_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_31013_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : human Kv4.2-DPP6S complex
Entire | Name: human Kv4.2-DPP6S complex |
---|---|
Components |
|
-Supramolecule #1: human Kv4.2-DPP6S complex
Supramolecule | Name: human Kv4.2-DPP6S complex / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() |
-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 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 86.392797 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: WKGIAIALLV ILVICSLIVT SVILLTPAED NSLSQKKKVT VEDLFSEDFK IHDPEAKWIS DTEFIYREQK GTVRLWNVET NTSTVLIEG KKIESLRAIR YEISPDREYA LFSYNVEPIY QHSYTGYYVL SKIPHGDPQS LDPPEVSNAK LQYAGWGPKG Q QLIFIFEN ...String: WKGIAIALLV ILVICSLIVT SVILLTPAED NSLSQKKKVT VEDLFSEDFK IHDPEAKWIS DTEFIYREQK GTVRLWNVET NTSTVLIEG KKIESLRAIR YEISPDREYA LFSYNVEPIY QHSYTGYYVL SKIPHGDPQS LDPPEVSNAK LQYAGWGPKG Q QLIFIFEN NIYYCAHVGK QAIRVVSTGK EGVIYNGLSD WLYEEEILKT HIAHWWSPDG TRLAYAAIND SRVPIMELPT YT GSIYPTV KPYHYPKAGS ENPSISLHVI GLNGPTHDLE MMPPDDPRMR EYYITMVKWA TSTKVAVTWL NRAQNVSILT LCD ATTGVC TKKHEDESEA WLHRQNEEPV FSKDGRKFFF IRAIPQGGRG KFYHITVSSS QPNSSNDNIQ SITSGDWDVT KILA YDEKG NKIYFLSTED LPRRRQLYSA NTVGNFNRQC LSCDLVENCT YFSASFSHSM DFFLLKCEGP GVPMVTVHNT TDKKK MFDL ETNEHVKKAI NDRQMPKVEY RDIEIDDYNL PMQILKPATF TDTTHYPLLL VVDGTPGSQS VAEKFEVSWE TVMVSS HGA VVVKCDGRGS GFQGTKLLHE VRRRLGLLEE KDQMEAVRTM LKEQYIDRTR VAVFGKDYGG YLSTYILPAK GENQGQT FT CGSALSPITD FKLYASAFSE RYLGLHGLDN RAYEMTKVAH RVSALEEQQF LIIHPTADEK IHFQHTAELI TQLIRGKA N YSLQIYPDES HYFTSSSLKQ HLYRSIINFF VECFRI |
-Macromolecule #2: Potassium voltage-gated channel subfamily D member 2
Macromolecule | Name: Potassium voltage-gated channel subfamily D member 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 45.297133 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DALIVLNVSG TRFQTWQDTL ERYPDTLLGS SERDFFYHPE TQQYFFDRDP DIFRHILNFY RTGKLHYPRH ECISAYDEEL AFFGLIPEI IGDCCYEEYK DRRRENAERL QDDADTDTAG ESALPTMTAR QRVWRAFENP HTSTMALVFY YVTGFFIAVS V IANVVETV ...String: DALIVLNVSG TRFQTWQDTL ERYPDTLLGS SERDFFYHPE TQQYFFDRDP DIFRHILNFY RTGKLHYPRH ECISAYDEEL AFFGLIPEI IGDCCYEEYK DRRRENAERL QDDADTDTAG ESALPTMTAR QRVWRAFENP HTSTMALVFY YVTGFFIAVS V IANVVETV PCGSSPGHIK ELPCGERYAV AFFCLDTACV MIFTVEYLLR LAAAPSRYRF VRSVMSIIDV VAILPYYIGL VM TDNEDVS GAFVTLRVFR VFRIFKFSRH SQGLRILGYT LKSCASELGF LLFSLTMAII IFATVMFYAE KGSSASKFTS IPA AFWYTI VTMTTLGYGD MVPKTIAGKI FGSICSLSGV LVIALPVPVI VSNFSRIYHQ NQRADKRRAQ KKARLARIRA AK |
-Macromolecule #3: Potassium voltage-gated channel subfamily D member 2
Macromolecule | Name: Potassium voltage-gated channel subfamily D member 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 45.167953 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DALIVLNVSG TRFQTWQDTL ERYPDTLLGS SERDFFYHPE TQQYFFDRDP DIFRHILNFY RTGKLHYPRH ECISAYDEEL AFFGLIPEI IGDCCYEEYK DRRRENAERL QDDADTDTAG ESALPTMTAR QRVWRAFENP HTSTMALVFY YVTGFFIAVS V IANVVETV ...String: DALIVLNVSG TRFQTWQDTL ERYPDTLLGS SERDFFYHPE TQQYFFDRDP DIFRHILNFY RTGKLHYPRH ECISAYDEEL AFFGLIPEI IGDCCYEEYK DRRRENAERL QDDADTDTAG ESALPTMTAR QRVWRAFENP HTSTMALVFY YVTGFFIAVS V IANVVETV PCGSSPGHIK ELPCGERYAV AFFCLDTACV MIFTVEYLLR LAAAPSRYRF VRSVMSIIDV VAILPYYIGL VM TDNEDVS GAFVTLRVFR VFRIFKFSRH SQGLRILGYT LKSCASELGF LLFSLTMAII IFATVMFYAE KGSSASKFTS IPA AFWYTI VTMTTLGYGD MVPKTIAGKI FGSICSLSGV LVIALPVPVI VSNFSRIYHQ NQRADKRRAQ KKARLARIRA A |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
---|---|
Output model | ![]() PDB-7e8b: |