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- EMDB-9116: CryoEM reconstruction of native lens connexin-46/50 at 3.4 angstr... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9116 | |||||||||
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Title | CryoEM reconstruction of native lens connexin-46/50 at 3.4 angstrom resolution | |||||||||
![]() | Cx46/50 D6 symmetrized map, 3.4 angstrom resolution, sharpened | |||||||||
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Function / homology | ![]() gap junction hemi-channel activity / gap junction-mediated intercellular transport / connexin complex / gap junction channel activity / visual perception / cell-cell signaling / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Myers JB / Reichow SL | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of native lens connexin 46/50 intercellular channels by cryo-EM. Authors: Janette B Myers / Bassam G Haddad / Susan E O'Neill / Dror S Chorev / Craig C Yoshioka / Carol V Robinson / Daniel M Zuckerman / Steve L Reichow / ![]() ![]() Abstract: Gap junctions establish direct pathways for cell-to-cell communication through the assembly of twelve connexin subunits that form intercellular channels connecting neighbouring cells. Co-assembly of ...Gap junctions establish direct pathways for cell-to-cell communication through the assembly of twelve connexin subunits that form intercellular channels connecting neighbouring cells. Co-assembly of different connexin isoforms produces channels with unique properties and enables communication across cell types. Here we used single-particle cryo-electron microscopy to investigate the structural basis of connexin co-assembly in native lens gap junction channels composed of connexin 46 and connexin 50 (Cx46/50). We provide the first comparative analysis to connexin 26 (Cx26), which-together with computational studies-elucidates key energetic features governing gap junction permselectivity. Cx46/50 adopts an open-state conformation that is distinct from the Cx26 crystal structure, yet it appears to be stabilized by a conserved set of hydrophobic anchoring residues. 'Hot spots' of genetic mutations linked to hereditary cataract formation map to the core structural-functional elements identified in Cx46/50, suggesting explanations for many of the disease-causing effects. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 13.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.9 KB 20.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() | 11 KB 10.9 KB | Display Display | ![]() |
Images | ![]() | 139.2 KB | ||
Masks | ![]() ![]() | 125 MB 125 MB | ![]() | |
Others | ![]() ![]() ![]() | 20.1 MB 95.5 MB 95.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mhqMC ![]() 6mhyMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 774.5 Data #1: Unaligned frame stacks - MP38 dataset 01 [micrographs - multiframe] Data #2: Unaligned frame stacks - MP38 dataset 02 [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Cx46/50 D6 symmetrized map, 3.4 angstrom resolution, sharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.665 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Cx46/50 D6 symmetrized map, 3.5 angstrom resolution, sharpened
File | emd_9116_additional_1.map | ||||||||||||
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Annotation | Cx46/50 D6 symmetrized map, 3.5 angstrom resolution, sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Cx46/50 D6 symmetrized map, 3.5 angstrom resolution, unprocessed
File | emd_9116_additional_2.map | ||||||||||||
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Annotation | Cx46/50 D6 symmetrized map, 3.5 angstrom resolution, unprocessed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Cx46/50 D6 symmetrized map, 3.4 angstrom resolution, unprocessed
File | emd_9116_additional_3.map | ||||||||||||
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Annotation | Cx46/50 D6 symmetrized map, 3.4 angstrom resolution, unprocessed | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Connexin-46 gap junction
Entire | Name: Connexin-46 gap junction |
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Components |
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-Supramolecule #1: Connexin-46 gap junction
Supramolecule | Name: Connexin-46 gap junction / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() Location in cell: C-terminal truncated version isolated from lens core |
Molecular weight | Theoretical: 450 KDa |
-Macromolecule #1: Gap junction alpha-3 protein, connexin-46
Macromolecule | Name: Gap junction alpha-3 protein, connexin-46 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 37.968516 KDa |
Sequence | String: MGDWSFLGRL LENAQEHSTV IGKVWLTVLF IFRILVLGAA AEEVWGDEQS DFTCNTQQPG CENVCYDRAF PISHVRFWVL QIIFVSTPT LIYLGHVLHL VRMEEKRKER EEEPPKAAGP AEEHQDPAPV RDDRGKVRIA GALLRTYVFN IIFKTLFEVG F IAGQYFLY ...String: MGDWSFLGRL LENAQEHSTV IGKVWLTVLF IFRILVLGAA AEEVWGDEQS DFTCNTQQPG CENVCYDRAF PISHVRFWVL QIIFVSTPT LIYLGHVLHL VRMEEKRKER EEEPPKAAGP AEEHQDPAPV RDDRGKVRIA GALLRTYVFN IIFKTLFEVG F IAGQYFLY GFQLKPLYRC DRWPCPNTVD CFISRPTEKT IFILFMLAVA CVSLLLNVLE IYHLGWKKLK QGMTSPFRPD TP GSRAGSA KPMGGSPLLL PPNSAPPAVT IGFPPYYAPS ASSLGQASAP GYPEPPLPAA LPGTPGTPGT PGTLGGGGGN QGL RAPAQN CANREAEPQT SARKASPPAS TP |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.35 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV Details: 10 sec wait before blotting, 4.0 second blot before plunging. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 30 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 105000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |