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- EMDB-9570: C. elegans INX-6 gap junction hemichannel -

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Basic information

Entry
Database: EMDB / ID: EMD-9570
TitleC. elegans INX-6 gap junction hemichannel
Map data3D map of an INX-6 hemichannel
Sample
  • Complex: INX-6
    • Protein or peptide: Innexin-6
Keywordsinnexin / gap junction channel / octamer / wild type / TRANSPORT PROTEIN
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)
Methodsingle 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, 2016-
Header (metadata) releaseOct 26, 2016-
Map releaseDec 7, 2016-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5h1q
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9570.png

Downloads & links

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Map

FileDownload / File: emd_9570.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D map of an INX-6 hemichannel
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 160 pix.
= 196.8 Å		1.23 Å/pix.
x 160 pix.
= 196.8 Å		1.23 Å/pix.
x 160 pix.
= 196.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.10672728 - 0.16867076
Average (Standard dev.)0.000018914378 (±0.01083242)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 196.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z196.800196.800196.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ129141209
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1070.1690.000

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Supplemental data

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Sample components

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Entire : INX-6

EntireName: INX-6
Components
  • Complex: INX-6
    • Protein or peptide: Innexin-6

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Supramolecule #1: INX-6

SupramoleculeName: INX-6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Innexin-6

MacromoleculeName: Innexin-6 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 45.173766 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

UniProtKB: Innexin-6

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3000SFF
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 7.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 74398
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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