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Yorodumi- PDB-8s8z: Cryo-EM structure of octameric human CALHM1 (I109W) in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 8s8z | |||||||||
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Title | Cryo-EM structure of octameric human CALHM1 (I109W) in complex with ruthenium red | |||||||||
Components | Calcium homeostasis modulator protein 1 | |||||||||
Keywords | MEMBRANE PROTEIN / taste / assembly / calcium homeostasis modulator protein / channel / lipid binding / large-pore channel / ruthenium red | |||||||||
Function / homology | Function and homology information Sensory perception of salty taste / ATP transport / sensory perception of bitter taste / sensory perception of umami taste / sensory perception of sweet taste / protein heterooligomerization / voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / response to stimulus / regulation of monoatomic ion transmembrane transport ...Sensory perception of salty taste / ATP transport / sensory perception of bitter taste / sensory perception of umami taste / sensory perception of sweet taste / protein heterooligomerization / voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / response to stimulus / regulation of monoatomic ion transmembrane transport / monoatomic cation transport / voltage-gated calcium channel activity / monoatomic cation channel activity / protein homooligomerization / Sensory perception of sweet, bitter, and umami (glutamate) taste / basolateral plasma membrane / endoplasmic reticulum membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.91 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 | 8s8z.cif.gz | 367 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s8z.ent.gz | 302.1 KB | Display | PDB format |
PDBx/mmJSON format | 8s8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8s8z_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8s8z_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8s8z_validation.xml.gz | 78.6 KB | Display | |
Data in CIF | 8s8z_validation.cif.gz | 95.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/8s8z ftp://data.pdbj.org/pub/pdb/validation_reports/s8/8s8z | HTTPS FTP |
-Related structure data
Related structure data | 40232MC 8gmpC 8gmqC 8gmrC 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: 34842.539 Da / Num. of mol.: 8 / Mutation: I109W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALHM1, FAM26C / Cell line (production host): HEK293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q8IU99 #2: Chemical | ChemComp-POV / ( #3: Chemical | ChemComp-R2R / | 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 human CALHM1 (I109W) in complex with ruthenium red 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: LEICA EM GP / Cryogen name: ETHANE |
-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: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68351 / Symmetry type: POINT |