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Yorodumi- EMDB-40233: Cryo-EM structure of octameric human CALHM1 (I109W) in complex wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40233 | |||||||||
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Title | Cryo-EM structure of octameric human CALHM1 (I109W) in complex with ruthenium red (C1) | |||||||||
Map data | Cryo-EM map of human CALHM1 (I109W) in complex with ruthenium red (C1) | |||||||||
Sample |
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Keywords | taste / assembly / calcium homeostasis modulator protein / membrane 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 / regulation of monoatomic ion transmembrane transport / response to stimulus ...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 / regulation of monoatomic ion transmembrane transport / response to stimulus / 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: 4.73 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: Syrjanen JL / Epstein M / Gomez R / Furukawa H | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40233.map.gz | 103.4 MB | EMDB map data format | |
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Header (meta data) | emd-40233-v30.xml emd-40233.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_40233.png | 157.3 KB | ||
Others | emd_40233_half_map_1.map.gz emd_40233_half_map_2.map.gz | 115.7 MB 115.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40233 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40233 | HTTPS FTP |
-Related structure data
Related structure data | 8s90MC 8gmpC 8gmqC 8gmrC 8s8zC 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_40233.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM map of human CALHM1 (I109W) in complex with ruthenium red (C1) | ||||||||||||||||||||
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: half-map of human CALHM1 (I109W) in complex with ruthenium red (C1)
File | emd_40233_half_map_1.map | ||||||||||||
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Annotation | half-map of human CALHM1 (I109W) in complex with ruthenium red (C1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map of human CALHM1 (I109W) in complex with ruthenium red (C1)
File | emd_40233_half_map_2.map | ||||||||||||
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Annotation | half-map of human CALHM1 (I109W) in complex with ruthenium red (C1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Octameric human CALHM1 (I109W) in complex with ruthenium red (C1)
Entire | Name: Octameric human CALHM1 (I109W) in complex with ruthenium red (C1) |
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Components |
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-Supramolecule #1: Octameric human CALHM1 (I109W) in complex with ruthenium red (C1)
Supramolecule | Name: Octameric human CALHM1 (I109W) in complex with ruthenium red (C1) 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: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)
Macromolecule | Name: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2) type: ligand / ID: 2 / Number of copies: 1 / Formula: R2R |
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Molecular weight | Theoretical: 559.525 Da |
Chemical component information | ChemComp-R2R: |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, cryoSPARC) / Number images used: 68351 |