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- EMDB-3345: Hexadecameric structure of an invertebrate gap junction channel -

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Basic information

Entry
Database: EMDB / ID: EMD-3345
TitleHexadecameric structure of an invertebrate gap junction channel
Map dataThis is a map showing a single INX-6 gap junction channel with P2 crystallographic symmetry
Sample
  • Sample: The N-terminal deleted C. elegans innexin-6
  • Protein or peptide: innexin-6
Keywordsinnexin / gap junction channel / cryo-electron crystallography / three-dimensional reconstruction / two-dimensional crystal
Biological speciesCaenorhabditis elegans (invertebrata)
Methodelectron crystallography / cryo EM / Resolution: 10.0 Å
AuthorsOshima A / Matsuzawa T / Murata K / Tani K / Fujiyoshi Y
CitationJournal: J Mol Biol / Year: 2016
Title: Hexadecameric structure of an invertebrate gap junction channel.
Authors: Atsunori Oshima / Tomohiro Matsuzawa / Kazuyoshi Murata / Kazutoshi Tani / Yoshinori Fujiyoshi /
Abstract: Innexins are invertebrate-specific gap junction proteins with four transmembrane helices. These proteins oligomerize to constitute intercellular channels that allow for the passage of small signaling ...Innexins are invertebrate-specific gap junction proteins with four transmembrane helices. These proteins oligomerize to constitute intercellular channels that allow for the passage of small signaling molecules associated with neural and muscular electrical activity. In contrast to the large number of structural and functional studies of connexin gap junction channels, few structural studies of recombinant innexin channels are reported. Here we show the three-dimensional structure of two-dimensionally crystallized Caenorhabditis elegans innexin-6 (INX-6) gap junction channels. The N-terminal deleted INX-6 proteins are crystallized in lipid bilayers. The three-dimensional reconstruction determined by cryo-electron crystallography reveals that a single INX-6 gap junction channel comprises 16 subunits, a hexadecamer, in contrast to chordate connexin channels, which comprise 12 subunits. The channel pore diameters at the cytoplasmic entrance and extracellular gap region are larger than those of connexin26. Two bulb densities are observed in each hemichannel, one in the pore and the other at the cytoplasmic side of the hemichannel in the channel pore pathway. These findings imply a structural diversity of gap junction channels among multicellular organisms.
History
DepositionFeb 25, 2016-
Header (metadata) releaseMar 23, 2016-
Map releaseMar 23, 2016-
UpdateMay 4, 2016-
Current statusMay 4, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3345.tif

Downloads & links

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Map

FileDownload / File: emd_3345.map.gz / Format: CCP4 / Size: 2.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map showing a single INX-6 gap junction channel with P2 crystallographic symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
2.5 Å/pix.
x 129 pix.
= 322.5 Å		2.44 Å/pix.
x 69 pix.
= 168.339 Å		2.52 Å/pix.
x 63 pix.
= 158.615 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX: 2.4397 Å / Y: 2.5177 Å / Z: 2.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 1
Minimum - Maximum-7.99069977 - 4.11950016
Average (Standard dev.)-0.0170252 (±0.98647678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-34-31-64
Dimensions6963129
Spacing6369129
CellA: 168.3393 Å / B: 158.6151 Å / C: 322.5 Å
α: 90.0 ° / β: 90.0 ° / γ: 121.7 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.43969565217392.51769841269842.5
M x/y/z6963129
origin x/y/z0.0000.0000.000
length x/y/z168.339158.615322.500
α/β/γ90.00090.000121.700
start NX/NY/NZ-34-31-64
NX/NY/NZ6963129
MAP C/R/S213
start NC/NR/NS-31-34-64
NC/NR/NS6369129
D min/max/mean-7.9914.120-0.017

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Supplemental data

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Sample components

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Entire : The N-terminal deleted C. elegans innexin-6

EntireName: The N-terminal deleted C. elegans innexin-6
Components
  • Sample: The N-terminal deleted C. elegans innexin-6
  • Protein or peptide: innexin-6

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Supramolecule #1000: The N-terminal deleted C. elegans innexin-6

SupramoleculeName: The N-terminal deleted C. elegans innexin-6 / type: sample / ID: 1000 / Details: The sample was reconstituted in lipid bilayers. / Oligomeric state: hexadecamer / Number unique components: 1
Molecular weightExperimental: 700 KDa / Theoretical: 700 KDa / Method: MALDI-TOF

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Macromolecule #1: innexin-6

MacromoleculeName: innexin-6 / type: protein_or_peptide / ID: 1 / Name.synonym: INX-6 / Number of copies: 16 / Oligomeric state: 16 / Recombinant expression: Yes
Source (natural)Organism: Caenorhabditis elegans (invertebrata) / synonym: roundworm
Molecular weightExperimental: 700 KDa / Theoretical: 700 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 / Recombinant plasmid: pFastbac

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state2D array

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 10 mM Tris (pH 7.5), 500 mM NaCl, and 1 mM EDTA
VitrificationCryogen name: ETHANE / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 30 seconds before plunging
DetailsDialysis
Crystal formationDetails: Dialysis

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Electron microscopy

MicroscopeJEOL KYOTO-3000SFF
TemperatureMin: 4 K / Max: 20 K / Average: 4 K
DateJul 26, 2014
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 249 / Average electron dose: 20 e/Å2 / Camera length: 2000 / Bits/pixel: 8
Tilt angle min0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38210 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 3.459 µm / Nominal defocus min: 0.66 µm / Nominal magnification: 40000
Sample stageSpecimen holder model: JEOL / Tilt angle max: 45 / Tilt series - Axis1 - Min angle: 0 ° / Tilt series - Axis1 - Max angle: 45 °

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Image processing

DetailsImages were processed with the MRC 2D crystal processing package.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: MRC
Crystal parametersUnit cell - A: 118.5 Å / Unit cell - B: 111.5 Å / Unit cell - C: 320 Å / Unit cell - γ: 121.7 ° / Unit cell - α: 90.0 ° / Unit cell - β: 90.0 ° / Plane group: P 2
CTF correctionDetails: Each micrograph

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