+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0938 | |||||||||
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Title | Structure of CLHM1 from Caenorhabditis Elegans | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information non-motile cilium / regulation of monoatomic ion transmembrane transport / regulation of locomotion / voltage-gated calcium channel activity / monoatomic cation channel activity / calcium ion transmembrane transport / plasma membrane Similarity search - Function | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.73 Å | |||||||||
Authors | Yang WX / Wang YW / Zhang XC | |||||||||
Funding support | China, 1 items
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Citation | Journal: Protein Sci / Year: 2020 Title: Cryo-electron microscopy structure of CLHM1 ion channel from Caenorhabditis elegans. Authors: Weixin Yang / Youwang Wang / Jianli Guo / Lingli He / Ye Zhou / Hui Zheng / Zhenfeng Liu / Ping Zhu / Xuejun C Zhang / Abstract: Calcium homeostasis modulators (CALHMs/CLHMs) comprise a family of pore-forming protein complexes assembling into voltage-gated, Ca -sensitive, nonselective channels. These complexes contain an ion- ...Calcium homeostasis modulators (CALHMs/CLHMs) comprise a family of pore-forming protein complexes assembling into voltage-gated, Ca -sensitive, nonselective channels. These complexes contain an ion-conduction pore sufficiently wide to permit the passing of ATP molecules serving as neurotransmitters. While their function and structure information is accumulating, the precise mechanisms of these channel complexes remain to be full understood. Here, we present the structure of the Caenorhabditis elegans CLHM1 channel in its open state solved through single-particle cryo-electron microscopy at 3.7-Å resolution. The transmembrane region of the channel structure of the dominant class shows an assembly of 10-fold rotational symmetry in one layer, and its cytoplasmic region is involved in additional twofold symmetrical packing in a tail-to-tail manner. Furthermore, we identified a series of amino acid residues critical for the regulation of CeCLHM1 channel using functional assays, electrophysiological analyses as well as structural-based analysis. Our structure and function analyses provide new insights into the mechanisms of CALHM channels. | |||||||||
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_0938.map.gz | 12 MB | EMDB map data format | |
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Header (meta data) | emd-0938-v30.xml emd-0938.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | emd_0938.png | 217.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0938 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0938 | HTTPS FTP |
-Validation report
Summary document | emd_0938_validation.pdf.gz | 366.4 KB | Display | EMDB validaton report |
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Full document | emd_0938_full_validation.pdf.gz | 366 KB | Display | |
Data in XML | emd_0938_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | emd_0938_validation.cif.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0938 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0938 | HTTPS FTP |
-Related structure data
Related structure data | 6lomMC 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_0938.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : predicted: CALHM1-like protein
Entire | Name: predicted: CALHM1-like protein |
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Components |
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-Supramolecule #1: predicted: CALHM1-like protein
Supramolecule | Name: predicted: CALHM1-like protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Calcium homeostasis modulator protein
Macromolecule | Name: Calcium homeostasis modulator protein / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Molecular weight | Theoretical: 37.308633 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MTTSINSVVT VFQNVFTNHG STLLNGILIA TTVGGQSLVR KLTFSCPCAY PLNIYHSLVF MFGPTAALLL IGITVNSTTW KLAHGFFFR VRDTRHSWKT TCVSWIEVLI QSSVAPIAWL FVVFLDGGYY RCYRSHEFCL ISDAILCKNS TILNSYASTS S FNKISDNG ...String: MTTSINSVVT VFQNVFTNHG STLLNGILIA TTVGGQSLVR KLTFSCPCAY PLNIYHSLVF MFGPTAALLL IGITVNSTTW KLAHGFFFR VRDTRHSWKT TCVSWIEVLI QSSVAPIAWL FVVFLDGGYY RCYRSHEFCL ISDAILCKNS TILNSYASTS S FNKISDNG KYCPPCICVP NPTDASYLEA ESQIYAWGLL LFSGVAAFLV ITCNRMCDKY TLVQRQYVET YKNVETQKFD AV AKEHASQ LAEHNARAFF GQKDWTKRDW DWVSGIPEVN NPLFARLRLI AAEKTQQTMY TPLQLWNDNK GYRIPQPDLQ LTQ IIVDET KED |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49000 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |