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- EMDB-74938: Ca2+ bound destabilized open state Connexin-46/50 -

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Basic information

Entry
Database: EMDB / ID: EMD-74938
TitleCa2+ bound destabilized open state Connexin-46/50
Map data
Sample
  • Complex: Ca2+ bound destabilized open state Connexin-46/50 gap junction
    • Protein or peptide: Gap junction alpha-3 protein
  • Ligand: CALCIUM ION
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water
Keywordscalcium regulation / channel gating / connexin / cryo-EM / gap junction / large-pore channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


gap junction-mediated intercellular transport / gap junction hemi-channel activity / connexin complex / gap junction channel activity / visual perception / cell-cell signaling / plasma membrane
Similarity search - Function
Gap junction alpha-3 protein (Cx46) / Gap junction alpha-8 protein (Cx50) / Gap junction alpha-8 protein (Cx50) / Connexin, C-terminal / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin ...Gap junction alpha-3 protein (Cx46) / Gap junction alpha-8 protein (Cx50) / Gap junction alpha-8 protein (Cx50) / Connexin, C-terminal / Connexin / Connexin, N-terminal / Connexin, conserved site / Gap junction protein, cysteine-rich domain / Connexin, N-terminal domain superfamily / Connexin / Connexins signature 1. / Connexins signature 2. / Connexin homologues / Gap junction channel protein cysteine-rich domain
Similarity search - Domain/homology
Gap junction alpha-8 protein / Gap junction alpha-3 protein
Similarity search - Component
Biological speciesOvis aries (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 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 / O'Neill SE / Jarodsky JM / Haddad BG / Reichow SL
History
DepositionJan 5, 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_74938.png

Downloads & links

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Map

FileDownload / File: emd_74938.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 280 pix.
= 249.004 Å		0.89 Å/pix.
x 280 pix.
= 249.004 Å		0.89 Å/pix.
x 280 pix.
= 249.004 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8893 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0025
Minimum - Maximum-0.010464042 - 0.031065319
Average (Standard dev.)-0.00022686624 (±0.0012727705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 249.004 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_74938_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74938_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74938_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ca2+ bound destabilized open state Connexin-46/50 gap junction

EntireName: Ca2+ bound destabilized open state Connexin-46/50 gap junction
Components
  • Complex: Ca2+ bound destabilized open state Connexin-46/50 gap junction
    • Protein or peptide: Gap junction alpha-3 protein
  • Ligand: CALCIUM ION
  • Ligand: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: water

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Supramolecule #1: Ca2+ bound destabilized open state Connexin-46/50 gap junction

SupramoleculeName: Ca2+ bound destabilized open state Connexin-46/50 gap junction
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Ovis aries (sheep)

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Macromolecule #1: Gap junction alpha-3 protein

MacromoleculeName: Gap junction alpha-3 protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Ovis aries (sheep)
Molecular weightTheoretical: 43.927871 KDa
SequenceString: (ACE)GDWSFLGRL LENAQEHSTV IGKVWLTVLF IFRILVLGAA AEEVWGDEQS DFTCNTQQPG CENVCYDRAF PISHVR FWV LQIIFVSTPT LIYLGHVLHL VRMEEKRKER EEEPPKAAGP AEEHQDPAPV RDDRGKVRIA GALLRTYVFN IIFKTLF EV GFIAGQYFLY ...String:
(ACE)GDWSFLGRL LENAQEHSTV IGKVWLTVLF IFRILVLGAA AEEVWGDEQS DFTCNTQQPG CENVCYDRAF PISHVR FWV LQIIFVSTPT LIYLGHVLHL VRMEEKRKER EEEPPKAAGP AEEHQDPAPV RDDRGKVRIA GALLRTYVFN IIFKTLF EV GFIAGQYFLY GFQLKPLYRC DRWPCPNTVD CFISRPTEKT IFILFMLAVA CVSLLLNVLE IYHLGWKKLK QGMTSPFR P DTPGSRAGSA KPMGGSPLLL PPNSAPPAVT IGFPPYYAPS ASSLGQASAP GYPEPPLPAA LPGTPGTPGT PGTLGGGGG NQGLRAPAQN CANREAEPQT SARKASPPAS TPPAAPAGGP QQFLPGGAAG SSGDSDGEGA VTAVELHAPP EPPADPGRSS KASKSSGGR ARAADLAI

UniProtKB: Gap junction alpha-3 protein

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 12 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 192 / Formula: MC3
Molecular weightTheoretical: 677.933 Da
Chemical component information

ChemComp-MC3:
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 540 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
2.0 mMC10H16N2O8EDTA
2.0 mMC14H24N2O10EGTA
150.0 mMNaClSodium Chloride
20.0 mMCaCl2Calcium chloride
GridModel: Quantifoil Active R2/1 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5750 / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3940202
CTF correctionSoftware - Name: RELION / Type: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 242797
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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Atomic model buiding 1

Initial modelPDB ID:

7jkc


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9zxx:
Ca2+ bound destabilized open state Connexin-46

PDB-9zy3:
Ca2+ bound destabilized open state Connexin-50

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