+Open data
-Basic information
Entry | Database: PDB / ID: 8gmq | |||||||||
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Title | Chicken CALHM1 purified from mammalian cells | |||||||||
Components | Calcium homeostasis modulator 1 | |||||||||
Keywords | MEMBRANE PROTEIN / taste / assembly / calcium homeostasis modulator protein / channel / lipid binding / large-pore channel | |||||||||
Function / homology | Calcium homeostasis modulator family / Calcium homeostasis modulator / membrane / Chem-POV / Calcium homeostasis modulator 1 Function and homology information | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Syrjanen, J.L. / Furukawa, H. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure of human CALHM1 reveals key locations for channel regulation and blockade by ruthenium red. Authors: Johanna L Syrjänen / Max Epstein / Ricardo Gómez / Hiro Furukawa / Abstract: Calcium homeostasis modulator 1 (CALHM1) is a voltage-dependent channel involved in neuromodulation and gustatory signaling. Despite recent progress in the structural biology of CALHM1, insights into ...Calcium homeostasis modulator 1 (CALHM1) is a voltage-dependent channel involved in neuromodulation and gustatory signaling. Despite recent progress in the structural biology of CALHM1, insights into functional regulation, pore architecture, and channel blockade remain limited. Here we present the cryo-EM structure of human CALHM1, revealing an octameric assembly pattern similar to the non-mammalian CALHM1s and the lipid-binding pocket conserved across species. We demonstrate by MD simulations that this pocket preferentially binds a phospholipid over cholesterol to stabilize its structure and regulate the channel activities. Finally, we show that residues in the amino-terminal helix form the channel pore that ruthenium red binds and blocks. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gmq.cif.gz | 340 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gmq.ent.gz | 282.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gmq_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8gmq_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8gmq_validation.xml.gz | 77.7 KB | Display | |
Data in CIF | 8gmq_validation.cif.gz | 97.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/8gmq ftp://data.pdbj.org/pub/pdb/validation_reports/gm/8gmq | HTTPS FTP |
-Related structure data
Related structure data | 40230MC 8gmpC 8gmrC 8s8zC 8s90C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 34065.785 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: CALHM1 / Cell line (production host): Hek293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: A0A8V0ZGE7 #2: Chemical | ChemComp-POV / ( Has ligand of interest | Y | |
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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: Octameric chicken CALHM1 with lipids / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Strain: HEK293 GnTI- |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 288.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
3D reconstruction | Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188439 / Symmetry type: POINT |