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Yorodumi- EMDB-0825: Human Cx31.3/GJC3 connexin hemichannel in the absence of calcium -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0825 | |||||||||
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Title | Human Cx31.3/GJC3 connexin hemichannel in the absence of calcium | |||||||||
Map data | postprocess-masked map | |||||||||
Sample |
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Keywords | Gap junction / Hemichannel / Hexamer / ATP release / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information connexin complex / gap junction channel activity / myelination / sensory perception of sound / cell-cell signaling / myelin sheath / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.34 Å | |||||||||
Authors | Lee HJ / Jeong H | |||||||||
Funding support | Korea, Republic Of, 1 items
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Citation | Journal: Sci Adv / Year: 2020 Title: Cryo-EM structure of human Cx31.3/GJC3 connexin hemichannel. Authors: Hyuk-Joon Lee / Hyeongseop Jeong / Jaekyung Hyun / Bumhan Ryu / Kunwoong Park / Hyun-Ho Lim / Jejoong Yoo / Jae-Sung Woo / Abstract: Connexin family proteins assemble into hexameric channels called hemichannels/connexons, which function as transmembrane channels or dock together to form gap junction intercellular channels (GJIChs). ...Connexin family proteins assemble into hexameric channels called hemichannels/connexons, which function as transmembrane channels or dock together to form gap junction intercellular channels (GJIChs). We determined the cryo-electron microscopy structures of human connexin 31.3 (Cx31.3)/GJC3 hemichannels in the presence and absence of calcium ions and with a hearing-loss mutation R15G at 2.3-, 2.5-, and 2.6-Å resolutions, respectively. Compared with available structures of GJICh in open conformation, Cx31.3 hemichannel shows substantial structural changes of highly conserved regions in the connexin family, including opening of calcium ion-binding tunnels, reorganization of salt-bridge networks, exposure of lipid-binding sites, and collocation of amino-terminal helices at the cytoplasmic entrance. We also found that the hemichannel has a pore with a diameter of ~8 Å and selectively transports chloride ions. Our study provides structural insights into the permeant selectivity of Cx31.3 hemichannel. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0825.map.gz | 12 MB | EMDB map data format | |
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Header (meta data) | emd-0825-v30.xml emd-0825.xml | 15 KB 15 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0825_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_0825.png | 163 KB | ||
Filedesc metadata | emd-0825.cif.gz | 5.4 KB | ||
Others | emd_0825_half_map_1.map.gz emd_0825_half_map_2.map.gz | 96.4 MB 96.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0825 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0825 | HTTPS FTP |
-Validation report
Summary document | emd_0825_validation.pdf.gz | 687.3 KB | Display | EMDB validaton report |
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Full document | emd_0825_full_validation.pdf.gz | 686.9 KB | Display | |
Data in XML | emd_0825_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_0825_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0825 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0825 | HTTPS FTP |
-Related structure data
Related structure data | 6l3tMC 0826C 0827C 6l3uC 6l3vC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0825.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | postprocess-masked map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.673 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half map 1
File | emd_0825_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_0825_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human Cx31.3/GJC3 connexin hemichannel in the absence of calcium
Entire | Name: Human Cx31.3/GJC3 connexin hemichannel in the absence of calcium |
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Components |
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-Supramolecule #1: Human Cx31.3/GJC3 connexin hemichannel in the absence of calcium
Supramolecule | Name: Human Cx31.3/GJC3 connexin hemichannel in the absence of calcium type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Gap junction gamma-3 protein
Macromolecule | Name: Gap junction gamma-3 protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 31.339365 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MCGRFLRRLL AEESRRSTPV GRLLLPVLLG FRLVLLAASG PGVYGDEQSE FVCHTQQPGC KAACFDAFHP LSPLRFWVFQ VILVAVPSA LYMGFTLYHV IWHWELSGKG KEEETLIQGR EGNTDVPGAG SLRLLWAYVA QLGARLVLEG AALGLQYHLY G FQMPSSFA ...String: MCGRFLRRLL AEESRRSTPV GRLLLPVLLG FRLVLLAASG PGVYGDEQSE FVCHTQQPGC KAACFDAFHP LSPLRFWVFQ VILVAVPSA LYMGFTLYHV IWHWELSGKG KEEETLIQGR EGNTDVPGAG SLRLLWAYVA QLGARLVLEG AALGLQYHLY G FQMPSSFA CRREPCLGSI TCNLSRPSEK TIFLKTMFGV SGFCLLFTFL ELVLLGLGRW WRTWKHKSSS SKYFLTSEST RR HKKATDS LPVVETKEQF QEAVPGRSLA QEKQRPVGPR DA UniProtKB: Gap junction gamma-3 protein |
-Macromolecule #2: Lauryl Maltose Neopentyl Glycol
Macromolecule | Name: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 2 / Number of copies: 6 / Formula: LMN |
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Molecular weight | Theoretical: 1.005188 KDa |
Chemical component information | ChemComp-AV0: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 204 / 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
Buffer | pH: 7.5 |
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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: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |