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- EMDB-78228: Calcium Bound Connexin-46/50 in Amphipol -

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Basic information

Entry
Database: EMDB / ID: EMD-78228
TitleCalcium Bound Connexin-46/50 in Amphipol
Map dataCalcium Bound Connexin-46/50 in Amphipol
Sample
  • Complex: Connexin-46/50 gap junction
    • Protein or peptide: Connexin-46/50
KeywordsConnexin-46/50 / calcium inhibition / MEMBRANE PROTEIN
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsJarodsky JM / Reichow SL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R35GM124779 United States
National Institutes of Health/National Eye Institute (NIH/NEI)F31EY030409 United States
CitationJournal: Nat Commun / Year: 2026
Title: Calcium induced N-terminal gating and pore collapse in connexin-46/50 gap junctions
Authors: Flores JA / Jarodsky JM / Haddad BG / Reichow SL
History
DepositionJul 23, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78228.png

Downloads & links

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Map

FileDownload / File: emd_78228.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCalcium Bound Connexin-46/50 in Amphipol
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065
Minimum - Maximum-0.13831611 - 0.4006836
Average (Standard dev.)0.0019167351 (±0.011021418)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map

Fileemd_78228_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_78228_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_78228_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Connexin-46/50 gap junction

EntireName: Connexin-46/50 gap junction
Components
  • Complex: Connexin-46/50 gap junction
    • Protein or peptide: Connexin-46/50

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Supramolecule #1: Connexin-46/50 gap junction

SupramoleculeName: Connexin-46/50 gap junction / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ovis aries (sheep)

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Macromolecule #1: Connexin-46/50

MacromoleculeName: Connexin-46/50 / type: protein_or_peptide / ID: 1
Details: These channels are made from connexin-46 and connexin-50 isoforms. The sequence entered is for the connexin-46 isoform
Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
SequenceString: MGDWSFLGRL LENAQEHSTV IGKVWLTVLF IFRILVLGAA AEEVWGDEQS DFTCNTQQPG CENVCYDRAF PISHVRFWVL QIIFVSTPTL IYLGHVLHLV RMEEKRKERE EEPPKAAGPA EEHQDPAPVR DDRGKVRIAG ALLRTYVFNI IFKTLFEVGF IAGQYFLYGF ...String:
MGDWSFLGRL LENAQEHSTV IGKVWLTVLF IFRILVLGAA AEEVWGDEQS DFTCNTQQPG CENVCYDRAF PISHVRFWVL QIIFVSTPTL IYLGHVLHLV RMEEKRKERE EEPPKAAGPA EEHQDPAPVR DDRGKVRIAG ALLRTYVFNI IFKTLFEVGF IAGQYFLYGF QLKPLYRCDR WPCPNTVDCF ISRPTEKTIF ILFMLAVACV SLLLNVLEIY HLGWKKLKQG MTSPFRPDTP GSRAGSAKPM GGSPLLLPPN SAPPAVTIGF PPYYAPSASS LGQASAPGYP EPPLPAALPG TPGTPGTPGT LGGGGGNQGL RAPAQNCANR EAEPQTSARK ASPPASTPPA APAGGPQQFL PGGAAGSSGD SDGEGAVTAV ELHAPPEPPA DPGRSSKASK SSGGRARAAD LAI

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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: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 51693
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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