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- EMDB-9973: Undocked hemichannel of an N-terminal deletion mutant of INX-6 in... -

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Basic information

Entry
Database: EMDB / ID: EMD-9973
TitleUndocked hemichannel of an N-terminal deletion mutant of INX-6 in a nanodisc
Map data
Sample
  • Complex: octameric complex of innexin-6
    • Protein or peptide: Innexin-6
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: 3.6 Å
AuthorsBurendei B / Shinozaki R / Watanabe M / Terada T / Tani K / Fujiyoshi Y / Oshima A
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
New Energy and Industrial Technology Development Organization (NEDO) Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) 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, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateMar 11, 2020-
Current statusMar 11, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kfh
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9973.png

Downloads & links

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Map

FileDownload / File: emd_9973.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 180 pix.
= 221.76 Å		1.23 Å/pix.
x 180 pix.
= 221.76 Å		1.23 Å/pix.
x 180 pix.
= 221.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.232 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.20297718 - 0.38388622
Average (Standard dev.)0.00005633573 (±0.01760455)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 221.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2321.2321.232
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z221.760221.760221.760
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.2030.3840.000

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Supplemental data

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Sample components

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Entire : octameric complex of innexin-6

EntireName: octameric complex of innexin-6
Components
  • Complex: octameric complex of innexin-6
    • Protein or peptide: Innexin-6

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Supramolecule #1: octameric complex of innexin-6

SupramoleculeName: octameric complex of innexin-6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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

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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 / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeJEOL 3000SFF
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 35.0 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

Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 54536
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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