+Open data
-Basic information
Entry | Database: PDB / ID: 6lom | ||||||
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Title | Structure of CLHM1 from Caenorhabditis Elegans | ||||||
Components | Calcium homeostasis modulator protein | ||||||
Keywords | MEMBRANE PROTEIN / complex | ||||||
Function / homology | Function and homology information ATP export / non-motile cilium / monoatomic ion channel complex / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å | ||||||
Authors | Yang, W.X. / Wang, Y.W. / Zhang, X.C. | ||||||
Funding support | China, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6lom.cif.gz | 955.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lom.ent.gz | 818.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lom.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lom_validation.pdf.gz | 939.5 KB | Display | wwPDB validaton report |
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Full document | 6lom_full_validation.pdf.gz | 1017.8 KB | Display | |
Data in XML | 6lom_validation.xml.gz | 143.9 KB | Display | |
Data in CIF | 6lom_validation.cif.gz | 190.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/6lom ftp://data.pdbj.org/pub/pdb/validation_reports/lo/6lom | HTTPS FTP |
-Related structure data
Related structure data | 0938MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 37308.633 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: clhm-1, C44B7.4 / Production host: Homo sapiens (human) / References: UniProt: Q18593 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: predicted: CALHM1-like protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49000 / Symmetry type: POINT |