+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13940 | |||||||||
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Title | human Connexin 26 dodecamer at 20mmHg PCO2, pH7.4 | |||||||||
Map data | dodecameric assembly of human connexin 26 in 20mmHg PCO2 at pH7.4 | |||||||||
Sample |
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Function / homology | Function and homology information Transport of connexons to the plasma membrane / response to human chorionic gonadotropin / gap junction-mediated intercellular transport / epididymis development / gap junction channel activity involved in cell communication by electrical coupling / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / astrocyte projection ...Transport of connexons to the plasma membrane / response to human chorionic gonadotropin / gap junction-mediated intercellular transport / epididymis development / gap junction channel activity involved in cell communication by electrical coupling / Oligomerization of connexins into connexons / Transport of connexins along the secretory pathway / gap junction assembly / connexin complex / astrocyte projection / Gap junction assembly / gap junction channel activity / gap junction / cellular response to glucagon stimulus / inner ear development / decidualization / endoplasmic reticulum-Golgi intermediate compartment / lateral plasma membrane / response to retinoic acid / cellular response to dexamethasone stimulus / response to progesterone / response to ischemia / sensory perception of sound / transmembrane transport / response to estradiol / cell-cell signaling / cellular response to oxidative stress / cell body / response to lipopolysaccharide / calcium ion binding / perinuclear region of cytoplasm / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||
Authors | Brotherton DH / Cameron AD / Savva CG / Ragan TJ | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Structure / Year: 2022 Title: Conformational changes and CO-induced channel gating in connexin26. Authors: Deborah H Brotherton / Christos G Savva / Timothy J Ragan / Nicholas Dale / Alexander D Cameron / Abstract: Connexins form large-pore channels that function either as dodecameric gap junctions or hexameric hemichannels to allow the regulated movement of small molecules and ions across cell membranes. ...Connexins form large-pore channels that function either as dodecameric gap junctions or hexameric hemichannels to allow the regulated movement of small molecules and ions across cell membranes. Opening or closing of the channels is controlled by a variety of stimuli, and dysregulation leads to multiple diseases. An increase in the partial pressure of carbon dioxide (PCO) has been shown to cause connexin26 (Cx26) gap junctions to close. Here, we use cryoelectron microscopy (cryo-EM) to determine the structure of human Cx26 gap junctions under increasing levels of PCO. We show a correlation between the level of PCO and the size of the aperture of the pore, governed by the N-terminal helices that line the pore. This indicates that CO alone is sufficient to cause conformational changes in the protein. Analysis of the conformational states shows that movements at the N terminus are linked to both subunit rotation and flexing of the transmembrane helices. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13940.map.gz | 14.8 MB | EMDB map data format | |
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Header (meta data) | emd-13940-v30.xml emd-13940.xml | 20.7 KB 20.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13940_fsc.xml | 15.3 KB | Display | FSC data file |
Images | emd_13940.png | 113.3 KB | ||
Others | emd_13940_half_map_1.map.gz emd_13940_half_map_2.map.gz | 250.5 MB 250.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13940 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13940 | HTTPS FTP |
-Related structure data
Related structure data | 7qetMC 7qeoC 7qeqC 7qerC 7qesC 7qeuC 7qevC 7qewC 7qeyC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13940.map.gz / Format: CCP4 / Size: 316.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | dodecameric assembly of human connexin 26 in 20mmHg PCO2 at pH7.4 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map 1 from D6 refinement of full data
File | emd_13940_half_map_1.map | ||||||||||||
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Annotation | half map 1 from D6 refinement of full data | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2 from D6 refinement of full dataset
File | emd_13940_half_map_2.map | ||||||||||||
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Annotation | half map 2 from D6 refinement of full dataset | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : dodecameric assembly of human connexion 26
Entire | Name: dodecameric assembly of human connexion 26 |
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Components |
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-Supramolecule #1: dodecameric assembly of human connexion 26
Supramolecule | Name: dodecameric assembly of human connexion 26 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Gap junction beta-2 protein
Macromolecule | Name: Gap junction beta-2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.713674 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MDWGTLQTIL GGVNKHSTSI GKIWLTVLFI FRIMILVVAA KEVWGDEQAD FVCNTLQPGC KNVCYDHYFP ISHIRLWALQ LIFVSTPAL LVAMHVAYRR HEKKRKFIKG EIKSEFKDIE EIKTQKVRIE GSLWWTYTSS IFFRVIFEAA FMYVFYVMYD G FSMQRLVK ...String: MDWGTLQTIL GGVNKHSTSI GKIWLTVLFI FRIMILVVAA KEVWGDEQAD FVCNTLQPGC KNVCYDHYFP ISHIRLWALQ LIFVSTPAL LVAMHVAYRR HEKKRKFIKG EIKSEFKDIE EIKTQKVRIE GSLWWTYTSS IFFRVIFEAA FMYVFYVMYD G FSMQRLVK CNAWPCPNTV DCFVSRPTEK TVFTVFMIAV SGICILLNVT ELCYLLIRYC SGKSKKPVLV PR |
-Macromolecule #2: DODECYL-BETA-D-MALTOSIDE
Macromolecule | Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 48 / Formula: LMT |
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Molecular weight | Theoretical: 510.615 Da |
Chemical component information | ChemComp-LMT: |
-Macromolecule #3: PHOSPHATIDYLETHANOLAMINE
Macromolecule | Name: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 12 / Formula: PTY |
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Molecular weight | Theoretical: 734.039 Da |
Chemical component information | ChemComp-PTY: |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 305 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.5 mg/mL | ||||||||||||||||||||||||||||||
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Buffer | pH: 7.4 Component:
Details: The buffer, except DDM and DTT, was prepared fresh from 10x stock on day of use. The basal buffer was filtered and de-gassed, and DDM and DTT added. The buffer was pH corrected at point of ...Details: The buffer, except DDM and DTT, was prepared fresh from 10x stock on day of use. The basal buffer was filtered and de-gassed, and DDM and DTT added. The buffer was pH corrected at point of use to 7.4 using 2.5% CO2 in 97.5% N2. | ||||||||||||||||||||||||||||||
Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP Details: 3 microlitres protein applied to grid, blot time 6 seconds, in 2.5% CO2/97.5%N2 atmosphere. | ||||||||||||||||||||||||||||||
Details | This sample monodisperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 3305 / Average exposure time: 3.0 sec. / Average electron dose: 45.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |