[English] 日本語
![](img/lk-miru.gif)
- EMDB-40232: Cryo-EM structure of octameric human CALHM1 (I109W) in complex wi... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of octameric human CALHM1 (I109W) in complex with ruthenium red | |||||||||
![]() | human CALHM1 (I109W) in complex with ruthenium red | |||||||||
![]() |
| |||||||||
![]() | taste / assembly / calcium homeostasis modulator protein / membrane protein / channel / lipid binding / large-pore channel / ruthenium red | |||||||||
Function / homology | ![]() Sensory perception of salty taste / ATP transport / sensory perception of bitter taste / sensory perception of umami taste / sensory perception of sweet taste / ATP export / protein heterooligomerization / voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / 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 / ATP export / protein heterooligomerization / voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.91 Å | |||||||||
![]() | Syrjanen JL / Furukawa H | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 117.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 14.8 KB 14.8 KB | Display Display | ![]() |
Images | ![]() | 146.6 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8s8zMC ![]() 8gmpC ![]() 8gmqC ![]() 8gmrC ![]() 8s90C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | human CALHM1 (I109W) in complex with ruthenium red | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.856 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: human CALHM1 (I109W) in complex with ruthenium red half map
File | emd_40232_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | human CALHM1 (I109W) in complex with ruthenium red half map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: human CALHM1 (I109W) in complex with ruthenium red half map
File | emd_40232_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | human CALHM1 (I109W) in complex with ruthenium red half map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Octameric human CALHM1 (I109W) in complex with ruthenium red
Entire | Name: Octameric human CALHM1 (I109W) in complex with ruthenium red |
---|---|
Components |
|
-Supramolecule #1: Octameric human CALHM1 (I109W) in complex with ruthenium red
Supramolecule | Name: Octameric human CALHM1 (I109W) in complex with ruthenium red type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: ![]() |
-Macromolecule #1: Calcium homeostasis modulator protein 1
Macromolecule | Name: Calcium homeostasis modulator protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 34.842539 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MMDKFRMIFQ FLQSNQESFM NGICGIMALA SAQMYSAFDF NCPCLPGYNA AYSAGILLAP PLVLFLLGLV MNNNVSMLAE EWKRPPGRR AKDPAVLRYM FCSMAQRALW APVVWVAVTL LDGKCFLCAF CTAVPVSALG NGSLAPGLPA PELARLLARV P CPEIYDGD ...String: MMDKFRMIFQ FLQSNQESFM NGICGIMALA SAQMYSAFDF NCPCLPGYNA AYSAGILLAP PLVLFLLGLV MNNNVSMLAE EWKRPPGRR AKDPAVLRYM FCSMAQRALW APVVWVAVTL LDGKCFLCAF CTAVPVSALG NGSLAPGLPA PELARLLARV P CPEIYDGD WLLAREVAVR YLRCISQALG WSFVLLTTLL AFVVRSVRPC FTQAAFLKSK YWSHYIDIER KLFDETCTEH AK AFAKVCI QQFFEAMNHD LELGHTNGTL ATAPASAAAP TTPDGAEEER EKLRGITDQG TMNRLLGSAW SHPQFEK UniProtKB: Calcium homeostasis modulator protein 1 |
-Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 2 / Number of copies: 8 / Formula: POV |
---|---|
Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ![]() ChemComp-POV: |
-Macromolecule #3: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)
Macromolecule | Name: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2) type: ligand / ID: 3 / Number of copies: 1 / Formula: R2R |
---|---|
Molecular weight | Theoretical: 559.525 Da |
Chemical component information | ![]() ChemComp-R2R: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, cryoSPARC) / Number images used: 68351 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |