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- EMDB-56608: Connexin 26 from L Paradoxa in GDN detergent - hemichannel focuss... -

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Basic information

Entry
Database: EMDB / ID: EMD-56608
TitleConnexin 26 from L Paradoxa in GDN detergent - hemichannel focussed conformation 1
Map dataLocally sharpened map from Phenix
Sample
  • Complex: Dodecameric gap junction channel for Connexin 26
    • Protein or peptide: Connexin 26
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: water
KeywordsConnexin / Gap Junction Channel / Ion Channel / MEMBRANE PROTEIN
Biological speciesLepidosiren paradoxa (South American lungfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsBrotherton DH / Cameron AD
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/P010393/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of Connexin 26 from L Paradoxa
Authors: Brotherton DH / Dale N / Cameron AD
History
DepositionFeb 6, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56608.png

Downloads & links

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Map

FileDownload / File: emd_56608.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally sharpened map from Phenix
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 280 pix.
= 233.8 Å		0.84 Å/pix.
x 280 pix.
= 233.8 Å		0.84 Å/pix.
x 280 pix.
= 233.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.016462013 - 0.032337353
Average (Standard dev.)0.00003514889 (±0.0014361214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 233.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56608_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map from relion postprocess

Fileemd_56608_additional_1.map
AnnotationUnsharpened map from relion_postprocess
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from relion refine

Fileemd_56608_half_map_1.map
AnnotationHalf map 1 from relion_refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from relion refine

Fileemd_56608_half_map_2.map
AnnotationHalf map 2 from relion_refine
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dodecameric gap junction channel for Connexin 26

EntireName: Dodecameric gap junction channel for Connexin 26
Components
  • Complex: Dodecameric gap junction channel for Connexin 26
    • Protein or peptide: Connexin 26
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: water

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Supramolecule #1: Dodecameric gap junction channel for Connexin 26

SupramoleculeName: Dodecameric gap junction channel for Connexin 26 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Classification was focussed on chains A-F
Source (natural)Organism: Lepidosiren paradoxa (South American lungfish)

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Macromolecule #1: Connexin 26

MacromoleculeName: Connexin 26 / type: protein_or_peptide / ID: 1
Details: Connexin 26 from Lepidosiren paradoxa with additional linker and His tag.
Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Lepidosiren paradoxa (South American lungfish)
Molecular weightTheoretical: 31.184395 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNWGTLQAFL GGVNKHSTSI GKIWLSVIFI FRVMILVVAA ERVWGDEQSD FVCNTLQPGC KNVCYDHYFP ISHIRLWCLQ LIFVSTPAL LVVMHVAYRR HEDKRAVLHQ DGELAEKSLQ QIKTQKVRIE GALWWTYVTS IFFRLLFEGA FMFAFYYIYN G FQMTRLVK ...String:
MNWGTLQAFL GGVNKHSTSI GKIWLSVIFI FRVMILVVAA ERVWGDEQSD FVCNTLQPGC KNVCYDHYFP ISHIRLWCLQ LIFVSTPAL LVVMHVAYRR HEDKRAVLHQ DGELAEKSLQ QIKTQKVRIE GALWWTYVTS IFFRLLFEGA FMFAFYYIYN G FQMTRLVK CDAWPCPNTV DCFISRPTEK TMFTIFMIVA SVVCILLNVS ELCYLVIKAC LRHGKQEKYS SSQSSLMSKG KE HQQNKMN EFLLTNQATS LVPRGSHHHH HH

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Macromolecule #2: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 12 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 24 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 288 / 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

Concentration1.6 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12277 / Average exposure time: 2.0 sec. / Average electron dose: 46.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1099552
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 57156
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-28mc:
Connexin 26 from L Paradoxa in GDN detergent - hemichannel focussed conformation 1

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