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Yorodumi- EMDB-40229: Cryo-EM structure of octameric human CALHM1 with a I109W point mu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40229 | |||||||||
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Title | Cryo-EM structure of octameric human CALHM1 with a I109W point mutation | |||||||||
Map data | A map of the human CALHM1 protein (I109W point mutation), C8 symmetry | |||||||||
Sample |
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Keywords | taste / assembly / calcium homeostasis modulator protein / membrane protein / channel / lipid binding / large-pore channel | |||||||||
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 / 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 | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Syrjanen JL / Furukawa H | |||||||||
Funding support | United States, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40229.map.gz | 97.4 MB | EMDB map data format | |
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Header (meta data) | emd-40229-v30.xml emd-40229.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40229_fsc.xml | 14.6 KB | Display | FSC data file |
Images | emd_40229.png | 91.5 KB | ||
Filedesc metadata | emd-40229.cif.gz | 5.5 KB | ||
Others | emd_40229_half_map_1.map.gz emd_40229_half_map_2.map.gz | 115.7 MB 115.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40229 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40229 | HTTPS FTP |
-Validation report
Summary document | emd_40229_validation.pdf.gz | 808.6 KB | Display | EMDB validaton report |
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Full document | emd_40229_full_validation.pdf.gz | 808.1 KB | Display | |
Data in XML | emd_40229_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_40229_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40229 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40229 | HTTPS FTP |
-Related structure data
Related structure data | 8gmpMC 8gmqC 8gmrC 8s8zC 8s90C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_40229.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | A map of the human CALHM1 protein (I109W point mutation), C8 symmetry | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.856 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: A half-map of the human CALHM1 protein (I109W point mutation)
File | emd_40229_half_map_1.map | ||||||||||||
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Annotation | A half-map of the human CALHM1 protein (I109W point mutation) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: A half-map of the human CALHM1 protein (I109W point mutation)
File | emd_40229_half_map_2.map | ||||||||||||
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Annotation | A half-map of the human CALHM1 protein (I109W point mutation) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Octameric human CALHM1 (I109W)
Entire | Name: Octameric human CALHM1 (I109W) |
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Components |
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-Supramolecule #1: Octameric human CALHM1 (I109W)
Supramolecule | Name: Octameric human CALHM1 (I109W) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-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 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 34.842539 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
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 |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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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: FIELD EMISSION GUN |
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 |