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- PDB-5h1q: C. elegans INX-6 gap junction hemichannel -

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Basic information

Entry
Database: PDB / ID: 5h1q
TitleC. elegans INX-6 gap junction hemichannel
ComponentsInnexin-6
KeywordsTRANSPORT PROTEIN / innexin / gap junction channel / octamer / wild type
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: 3.3 Å
AuthorsOshima, A. / Tani, K. / Fujiyoshi, Y.
CitationJournal: Nat Commun / Year: 2016
Title: Atomic structure of the innexin-6 gap junction channel determined by cryo-EM.
Authors: Atsunori Oshima / Kazutoshi Tani / Yoshinori Fujiyoshi /
Abstract: Innexins, a large protein family comprising invertebrate gap junction channels, play an essential role in nervous system development and electrical synapse formation. Here we report the cryo-electron ...Innexins, a large protein family comprising invertebrate gap junction channels, play an essential role in nervous system development and electrical synapse formation. Here we report the cryo-electron microscopy structures of Caenorhabditis elegans innexin-6 (INX-6) gap junction channels at atomic resolution. We find that the arrangements of the transmembrane helices and extracellular loops of the INX-6 monomeric structure are highly similar to those of connexin-26 (Cx26), despite the lack of significant sequence similarity. The INX-6 gap junction channel comprises hexadecameric subunits but reveals the N-terminal pore funnel, consistent with Cx26. The helix-rich cytoplasmic loop and C-terminus are intercalated one-by-one through an octameric hemichannel, forming a dome-like entrance that interacts with N-terminal loops in the pore. These observations suggest that the INX-6 cytoplasmic domains are cooperatively associated with the N-terminal funnel conformation, and an essential linkage of the N-terminal with channel activity is presumably preserved across gap junction families.
History
DepositionOct 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Other

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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
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area30690 Å2
ΔGint-139 kcal/mol
Surface area134350 Å2

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Components

#1: Protein
Innexin-6 / Protein opu-6


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 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9U3N4

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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: INX-6 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pFastBac1
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM softwareName: RELION / Version: 1.4 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74398 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00824488
ELECTRON MICROSCOPYf_angle_d1.00133360
ELECTRON MICROSCOPYf_dihedral_angle_d11.15819408
ELECTRON MICROSCOPYf_chiral_restr0.0593680
ELECTRON MICROSCOPYf_plane_restr0.0054128

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