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- PDB-6kff: Undocked INX-6 hemichannel in a nanodisc -

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Basic information

Entry
Database: PDB / ID: 6kff
TitleUndocked INX-6 hemichannel in a nanodisc
ComponentsInnexin-6
KeywordsTRANSPORT PROTEIN / Gap junctions / Innexin
Function / homologygap 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 speciesCaenorhabditis elegans (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBurendei, B. / Shinozaki, R. / Watanabe, M. / Terada, T. / Tani, K. / Fujiyoshi, Y. / Oshima, A.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
New Energy and Industrial Technology Development Organization (NEDO) Japan
CitationJournal: 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
DepositionJul 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Feb 12, 2020Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Feb 12, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
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Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
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Revision 1.3Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
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Structure visualization

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Assembly

Deposited unit
A: Innexin-6
B: Innexin-6
C: Innexin-6
D: Innexin-6
E: Innexin-6
F: Innexin-6
G: Innexin-6
H: Innexin-6


Theoretical massNumber of molelcules
Total (without water)361,3908
Polymers361,3908
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area26000 Å2
ΔGint-141 kcal/mol
Surface area124260 Å2

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Components

#1: Protein
Innexin-6 / Protein opu-6 / innexin-6 gap junction 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 modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: octameric complex of innexin-6 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL 3000SFF
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
8PHENIXmodel refinement
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40359 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421832
ELECTRON MICROSCOPYf_angle_d0.5929744
ELECTRON MICROSCOPYf_dihedral_angle_d10.82112432
ELECTRON MICROSCOPYf_chiral_restr0.0383288
ELECTRON MICROSCOPYf_plane_restr0.0033632

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