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Yorodumi- EMDB-33399: Consensus map of connexin43/Cx43/GJA1 gap junction intercellular ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33399 | |||||||||
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Title | Consensus map of connexin43/Cx43/GJA1 gap junction intercellular channel in LMNG/CHS detergents at pH ~6.9 | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Lee HJ / Cha HJ / Jeong H / Lee SN / Lee CW / Woo JS | |||||||||
Funding support | Korea, Republic Of, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Conformational changes in the human Cx43/GJA1 gap junction channel visualized using cryo-EM. Authors: Hyuk-Joon Lee / Hyung Jin Cha / Hyeongseop Jeong / Seu-Na Lee / Chang-Won Lee / Minsoo Kim / Jejoong Yoo / Jae-Sung Woo / Abstract: Connexin family proteins assemble into hexameric hemichannels in the cell membrane. The hemichannels dock together between two adjacent membranes to form gap junction intercellular channels (GJIChs). ...Connexin family proteins assemble into hexameric hemichannels in the cell membrane. The hemichannels dock together between two adjacent membranes to form gap junction intercellular channels (GJIChs). We report the cryo-electron microscopy structures of Cx43 GJICh, revealing the dynamic equilibrium state of various channel conformations in detergents and lipid nanodiscs. We identify three different N-terminal helix conformations of Cx43-gate-covering (GCN), pore-lining (PLN), and flexible intermediate (FIN)-that are randomly distributed in purified GJICh particles. The conformational equilibrium shifts to GCN by cholesteryl hemisuccinates and to PLN by C-terminal truncations and at varying pH. While GJIChs that mainly comprise GCN protomers are occluded by lipids, those containing conformationally heterogeneous protomers show markedly different pore sizes. We observe an α-to-π-helix transition in the first transmembrane helix, which creates a side opening to the membrane in the FIN and PLN conformations. This study provides basic structural information to understand the mechanisms of action and regulation of Cx43 GJICh. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33399.map.gz | 27.7 MB | EMDB map data format | |
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Header (meta data) | emd-33399-v30.xml emd-33399.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33399_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_33399.png | 38.5 KB | ||
Others | emd_33399_half_map_1.map.gz emd_33399_half_map_2.map.gz | 192.4 MB 192.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33399 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33399 | HTTPS FTP |
-Validation report
Summary document | emd_33399_validation.pdf.gz | 892.8 KB | Display | EMDB validaton report |
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Full document | emd_33399_full_validation.pdf.gz | 892.4 KB | Display | |
Data in XML | emd_33399_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | emd_33399_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33399 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33399 | HTTPS FTP |
-Related structure data
Related structure data | 7f92C 7f93C 7f94C 7xq9C 7xqbC 7xqdC 7xqfC 7xqgC 7xqhC 7xqiC 7xqjC C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33399.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.675 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map
File | emd_33399_half_map_1.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map
File | emd_33399_half_map_2.map | ||||||||||||
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Annotation | half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dodecameric complex of human Cx43/GJA1 in detergents (LMNG/CHS) a...
Entire | Name: Dodecameric complex of human Cx43/GJA1 in detergents (LMNG/CHS) at pH ~6.9 |
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Components |
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-Supramolecule #1: Dodecameric complex of human Cx43/GJA1 in detergents (LMNG/CHS) a...
Supramolecule | Name: Dodecameric complex of human Cx43/GJA1 in detergents (LMNG/CHS) at pH ~6.9 type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all Details: Human Cx43 gap junction channel composed of two different protomers in pore-lining and gate-covering NTH conformations |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Gap junction alpha-1 protein (Cx43)
Macromolecule | Name: Gap junction alpha-1 protein (Cx43) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG CENVCYDKSF PISHVRFWVL QIIFVSVPTL LYLAHVFYVM RKEEKLNKKE EELKVAQTDG VNVDMHLKQI EIKKFKYGIE EHGKVKMRGG LLRTYIISIL FKSIFEVAFL ...String: MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG CENVCYDKSF PISHVRFWVL QIIFVSVPTL LYLAHVFYVM RKEEKLNKKE EELKVAQTDG VNVDMHLKQI EIKKFKYGIE EHGKVKMRGG LLRTYIISIL FKSIFEVAFL LIQWYIYGFS LSAVYTCKRD PCPHQVDCFL SRPTEKTIFI IFMLVVSLVS LALNIIELFY VFFKGVKDRV KGKSDPYHAT SGALSPAKDC GSQKYAYFNG CSSPTAPLSP MSPPGYKLVT GDRNNSSCRN YNKQASEQNW ANYSAEQNRM GQAGSTISNS HAQPFDFPDD NQNSKKLAAG HELQPLAIVD QRPSSRASSR ASSRPRPDDL EI |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.9 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.25 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |