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Yorodumi- EMDB-10924: Cryo-EM structure of decameric human CALHM6 in the presence of Ca2+ -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10924 | |||||||||
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Title | Cryo-EM structure of decameric human CALHM6 in the presence of Ca2+ | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Calcium homeostasis modulator protein 6 / Calcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic cation channel activity / plasma membrane / Calcium homeostasis modulator protein 6 Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.39 Å | |||||||||
Authors | Sawicka M / Drozdzyk K / Dutzler R | |||||||||
Funding support | 1 items
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Citation | Journal: Elife / Year: 2020 Title: Cryo-EM structures and functional properties of CALHM channels of the human placenta. Authors: Katarzyna Drożdżyk / Marta Sawicka / Maria-Isabel Bahamonde-Santos / Zaugg Jonas / Dawid Deneka / Christiane Albrecht / Raimund Dutzler / Abstract: The transport of substances across the placenta is essential for the development of the fetus. Here, we were interested in the role of channels of the calcium homeostasis modulator (CALHM) family in ...The transport of substances across the placenta is essential for the development of the fetus. Here, we were interested in the role of channels of the calcium homeostasis modulator (CALHM) family in the human placenta. By transcript analysis, we found the paralogs CALHM2, 4, and 6 to be highly expressed in this organ and upregulated during trophoblast differentiation. Based on electrophysiology, we observed that activation of these paralogs differs from the voltage- and calcium-gated channel CALHM1. Cryo-EM structures of CALHM4 display decameric and undecameric assemblies with large cylindrical pore, while in CALHM6 a conformational change has converted the pore shape into a conus that narrows at the intracellular side, thus describing distinct functional states of the channel. The pore geometry alters the distribution of lipids, which occupy the cylindrical pore of CALHM4 in a bilayer-like arrangement whereas they have redistributed in the conical pore of CALHM6 with potential functional consequences. | |||||||||
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_10924.map.gz | 4.4 MB | EMDB map data format | |
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Header (meta data) | emd-10924-v30.xml emd-10924.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10924_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_10924.png | 90.3 KB | ||
Masks | emd_10924_msk_1.map | 30.5 MB | Mask map | |
Others | emd_10924_additional.map.gz emd_10924_half_map_1.map.gz emd_10924_half_map_2.map.gz | 28.5 MB 22.3 MB 22.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10924 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10924 | HTTPS FTP |
-Validation report
Summary document | emd_10924_validation.pdf.gz | 425.1 KB | Display | EMDB validaton report |
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Full document | emd_10924_full_validation.pdf.gz | 424.3 KB | Display | |
Data in XML | emd_10924_validation.xml.gz | 12.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10924 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10924 | HTTPS FTP |
-Related structure data
Related structure data | 6ytvMC 6ytkC 6ytlC 6ytoC 6ytqC 6ytxC 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_10924.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.34 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 | emd_10924_msk_1.map | ||||||||||||
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Density Histograms |
-Additional map: #1
File | emd_10924_additional.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_10924_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_10924_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : Decameric CALHM6
Entire | Name: Decameric CALHM6 |
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Components |
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-Supramolecule #1: Decameric CALHM6
Supramolecule | Name: Decameric CALHM6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Calcium homeostasis modulator protein 6
Macromolecule | Name: Calcium homeostasis modulator protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 34.494109 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MEKFRAVLDL HVKHHSALGY GLVTLLTAGG ERIFSAVAFQ CPCSAAWNLP YGLVFLLVPA LALFLLGYVL SARTWRLLTG CCSSARASC GSALRGSLVC TQISAAAALA PLTWVAVALL GGAFYECAAT GSAAFAQRLC LGRNRSCAAE LPLVPCNQAK A SDVQDLLK ...String: MEKFRAVLDL HVKHHSALGY GLVTLLTAGG ERIFSAVAFQ CPCSAAWNLP YGLVFLLVPA LALFLLGYVL SARTWRLLTG CCSSARASC GSALRGSLVC TQISAAAALA PLTWVAVALL GGAFYECAAT GSAAFAQRLC LGRNRSCAAE LPLVPCNQAK A SDVQDLLK DLKAQSQVLG WILIAVVIII LLIFTSVTRC LSPVSFLQLK FWKIYLEQEQ QILKSKATEH ATELAKENIK CF FEGSHPK EYNTPSMKEW QQISSLYTFN PKGQYYSMLH KYVNRKEKTH SIRSTEGDTV IPVLGFVDSS GINSTPEL |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (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 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |