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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 / ATP export / voltage-gated monoatomic ion channel activity / regulation of monoatomic ion transmembrane transport / calcium-activated cation channel activity ...Sensory perception of salty taste / ATP transport / sensory perception of bitter taste / sensory perception of umami taste / sensory perception of sweet taste / protein heterooligomerization / ATP export / voltage-gated monoatomic ion channel activity / regulation of monoatomic ion transmembrane transport / calcium-activated cation channel activity / plasma membrane raft / monoatomic cation transport / monoatomic cation channel activity / voltage-gated calcium 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: 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
DepositionMar 27, 2023-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40233.png

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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 273.92 Å		0.86 Å/pix.
x 320 pix.
= 273.92 Å		0.86 Å/pix.
x 320 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
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

Histogram

Histogram (log scale)

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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

Histogram

Histogram (log scale)

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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)

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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
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

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

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