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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9971 | ||||||||||||
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Title | Undocked INX-6 hemichannel in a nanodisc | ||||||||||||
![]() | hemichannel INX-6 in a nanodisc | ||||||||||||
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Function / homology | gap junction hemi-channel activity / Innexin / Innexin / Pannexin family profile. / gap junction / gap junction channel activity / monoatomic ion transmembrane transport / plasma membrane / Innexin-6![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
![]() | Burendei B / Shinozaki R / Watanabe M / Terada T / Tani K / Fujiyoshi Y / Oshima A | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of undocked innexin-6 hemichannels in phospholipids. Authors: Batuujin Burendei / Ruriko Shinozaki / Masakatsu Watanabe / Tohru Terada / Kazutoshi Tani / Yoshinori Fujiyoshi / Atsunori Oshima / ![]() Abstract: Gap junctions form intercellular conduits with a large pore size whose closed and open states regulate communication between adjacent cells. The structural basis of the mechanism by which gap ...Gap junctions form intercellular conduits with a large pore size whose closed and open states regulate communication between adjacent cells. The structural basis of the mechanism by which gap junctions close, however, remains uncertain. Here, we show the cryo-electron microscopy structures of innexin-6 (INX-6) gap junction proteins in an undocked hemichannel form. In the nanodisc-reconstituted structure of the wild-type INX-6 hemichannel, flat double-layer densities obstruct the channel pore. Comparison of the hemichannel structures of a wild-type INX-6 in detergent and nanodisc-reconstituted amino-terminal deletion mutant reveals that lipid-mediated amino-terminal rearrangement and pore obstruction occur upon nanodisc reconstitution. Together with molecular dynamics simulations and electrophysiology functional assays, our results provide insight into the closure of the INX-6 hemichannel in a lipid bilayer before docking of two hemichannels. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 20.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.3 KB 10.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.3 KB | Display | ![]() |
Images | ![]() | 234.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kffMC ![]() 9972C ![]() 9973C ![]() 6kfgC ![]() 6kfhC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 49.5 Data #1: C. elegans T INX-6 undocked hemichannels in nanodiscs [micrographs - single frame]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | hemichannel INX-6 in a nanodisc | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.232 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : octameric complex of innexin-6
Entire | Name: octameric complex of innexin-6 |
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Components |
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-Supramolecule #1: octameric complex of innexin-6
Supramolecule | Name: octameric complex of innexin-6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Innexin-6
Macromolecule | Name: Innexin-6 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 45.173766 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MASQVGAINS VNALISRVFV QPKGDLADRL NSRVTVVILA VSSALLLSSH FIGDPITCWT PAQFNAQWVN FVNQYCFVHG TYFVPLDQQ LAFEEEERTK VSIQYYQWVP YVFALQAFLF YIPRFIWKAM IAYSGYDLAA AVKYVDRFWS ENRDKDDKFK T RLAAFEGR ...String: MASQVGAINS VNALISRVFV QPKGDLADRL NSRVTVVILA VSSALLLSSH FIGDPITCWT PAQFNAQWVN FVNQYCFVHG TYFVPLDQQ LAFEEEERTK VSIQYYQWVP YVFALQAFLF YIPRFIWKAM IAYSGYDLAA AVKYVDRFWS ENRDKDDKFK T RLAAFEGR PSVYIWDGIR LARKKRSRNM ALFYTLSTVW QAVNAWIQFY ILTQLLDSSI YTLWGPSILG DLLQGNDWQT TG HFPRIVH CDFNRRRPAS VQLDTVLCVL TLNIYYEKLF IFLWFWLVFV AVVSTVNCFK WIYYLCNKTK AQKTIKNYLS TAP IKSTIS DDQFFSALGE DGLFIMDQMA LNLGDIPASY LTISMRNICQ DFIESEDYID EERTPFVKSI KHT |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy
Microscope | JEOL 3000SFF |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |