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- PDB-5h1r: C. elegans INX-6 gap junction channel -

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Basic information

Entry
Database: PDB / ID: 5h1r
TitleC. elegans INX-6 gap junction channel
ComponentsInnexin-6
KeywordsTRANSPORT PROTEIN / innexin / gap junction channel / 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: 3.6 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 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / em_image_scans / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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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
I: Innexin-6
J: Innexin-6
K: Innexin-6
L: Innexin-6
M: Innexin-6
N: Innexin-6
O: Innexin-6
P: Innexin-6


Theoretical massNumber of molelcules
Total (without water)722,78016
Polymers722,78016
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area76100 Å2
ΔGint-332 kcal/mol
Surface area264470 Å2

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Components

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


Mass: 45173.766 Da / Num. of mol.: 16
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
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: 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_1496: / Classification: refinement
EM softwareName: RELION / Version: 1.4 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: D8 (2x8 fold dihedral)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35608 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01448848
ELECTRON MICROSCOPYf_angle_d1.33666544
ELECTRON MICROSCOPYf_dihedral_angle_d12.18538704
ELECTRON MICROSCOPYf_chiral_restr0.0667328
ELECTRON MICROSCOPYf_plane_restr0.0078240

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