+Open data
-Basic information
Entry | Database: PDB / ID: 6kff | ||||||||||||
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Title | Undocked INX-6 hemichannel in a nanodisc | ||||||||||||
Components | Innexin-6 | ||||||||||||
Keywords | TRANSPORT PROTEIN / Gap junctions / Innexin | ||||||||||||
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 Function and homology information | ||||||||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
Authors | Burendei, B. / Shinozaki, R. / Watanabe, M. / Terada, T. / Tani, K. / Fujiyoshi, Y. / Oshima, A. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Sci Adv / Year: 2020 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6kff.cif.gz | 459.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kff.ent.gz | 380.8 KB | Display | PDB format |
PDBx/mmJSON format | 6kff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kff_validation.pdf.gz | 1019.7 KB | Display | wwPDB validaton report |
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Full document | 6kff_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6kff_validation.xml.gz | 70.3 KB | Display | |
Data in CIF | 6kff_validation.cif.gz | 95.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/6kff ftp://data.pdbj.org/pub/pdb/validation_reports/kf/6kff | HTTPS FTP |
-Related structure data
Related structure data | 9971MC 9972C 9973C 6kfgC 6kfhC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10289 (Title: Cryo-EM structure of an undocked innexin-6 hemichannel in phospholipids Data size: 49.5 Data #1: C. elegans T INX-6 undocked hemichannels in nanodiscs [micrographs - single frame]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 45173.766 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: inx-6, opu-6, C36H8.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9U3N4 Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: octameric complex of innexin-6 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: JEOL 3000SFF |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: RELION / Version: 2 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Symmetry | Point symmetry: C8 (8 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40359 / Symmetry type: POINT | ||||||||||||||||||||||||
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