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- EMDB-40233: Cryo-EM structure of octameric human CALHM1 (I109W) in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-40233
TitleCryo-EM structure of octameric human CALHM1 (I109W) in complex with ruthenium red (C1)
Map dataCryo-EM map of human CALHM1 (I109W) in complex with ruthenium red (C1)
Sample
  • Complex: Octameric human CALHM1 (I109W) in complex with ruthenium red (C1)
    • Protein or peptide: Calcium homeostasis modulator protein 1
  • Ligand: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)
Keywordstaste / 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
Calcium homeostasis modulator family / Calcium homeostasis modulator
Similarity search - Domain/homology
Calcium homeostasis modulator protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.73 Å
AuthorsSyrjanen JL / Furukawa H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH) United States
CitationJournal: 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
DepositionMar 27, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_40233.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of human CALHM1 (I109W) in complex with ruthenium red (C1)
Voxel sizeX=Y=Z: 0.856 Å
Density
Contour LevelBy AUTHOR: 0.0736
Minimum - Maximum-0.17641178 - 0.3376361
Average (Standard dev.)0.0016477911 (±0.014510683)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map of human CALHM1 (I109W) in complex with ruthenium red (C1)

Fileemd_40233_half_map_1.map
Annotationhalf-map of human CALHM1 (I109W) in complex with ruthenium red (C1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: half-map of human CALHM1 (I109W) in complex with ruthenium red (C1)

Fileemd_40233_half_map_2.map
Annotationhalf-map of human CALHM1 (I109W) in complex with ruthenium red (C1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Octameric human CALHM1 (I109W) in complex with ruthenium red (C1)

EntireName: Octameric human CALHM1 (I109W) in complex with ruthenium red (C1)
Components
  • Complex: Octameric human CALHM1 (I109W) in complex with ruthenium red (C1)
    • Protein or peptide: Calcium homeostasis modulator protein 1
  • Ligand: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)

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Supramolecule #1: Octameric human CALHM1 (I109W) in complex with ruthenium red (C1)

SupramoleculeName: Octameric human CALHM1 (I109W) in complex with ruthenium red (C1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Calcium homeostasis modulator protein 1

MacromoleculeName: Calcium homeostasis modulator protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.842539 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #2: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)

MacromoleculeName: ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2)
type: ligand / ID: 2 / Number of copies: 1 / Formula: R2R
Molecular weightTheoretical: 559.525 Da
Chemical component information

ChemComp-R2R:
ruthenium(6+) azanide pentaamino(oxido)ruthenium (1/4/2) / Ruthenium red

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Image recordingFilm 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

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, cryoSPARC) / Number images used: 68351

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