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- EMDB-40230: Chicken CALHM1 purified from mammalian cells -

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Basic information

Entry
Database: EMDB / ID: EMD-40230
TitleChicken CALHM1 purified from mammalian cells
Map dataOctameric chicken CALHM1 structure expressed in and purified from a mammalian system.
Sample
  • Complex: Octameric chicken CALHM1 with lipids
    • Protein or peptide: Calcium homeostasis modulator 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Keywordstaste / assembly / calcium homeostasis modulator protein / membrane protein / channel / lipid binding / large-pore channel
Function / homologyCalcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic ion transport / membrane / Calcium homeostasis modulator 1
Function and homology information
Biological speciesHomo sapiens (human) / Gallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 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 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40230.png

Downloads & links

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Map

FileDownload / File: emd_40230.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOctameric chicken CALHM1 structure expressed in and purified from a mammalian system.
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: 2.21
Minimum - Maximum-5.0497007 - 11.135719
Average (Standard dev.)-0.01847652 (±0.37208846)
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 octameric chicken CALHM1 structure expressed in...

Fileemd_40230_half_map_1.map
AnnotationHalf-map of octameric chicken CALHM1 structure expressed in and purified from a mammalian system.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of octameric chicken CALHM1 structure expressed in...

Fileemd_40230_half_map_2.map
AnnotationHalf-map of octameric chicken CALHM1 structure expressed in and purified from a mammalian system.
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 chicken CALHM1 with lipids

EntireName: Octameric chicken CALHM1 with lipids
Components
  • Complex: Octameric chicken CALHM1 with lipids
    • Protein or peptide: Calcium homeostasis modulator 1
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

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Supramolecule #1: Octameric chicken CALHM1 with lipids

SupramoleculeName: Octameric chicken CALHM1 with lipids / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Calcium homeostasis modulator 1

MacromoleculeName: Calcium homeostasis modulator 1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 34.065785 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDKFRMVFQF LQSNQESFMS GICGIMALAS AQLYSAFDFN CPCLPRYNLA YGLGVLLVPP LILFLLGFVL NNNVSMLAEE WRRPQGQRQ KDAAVLRYMF CSMVQRAMIA PAVWVSVTLL DGKCITCAFC TSLPVEALGN ASHHGLPQGE VKRVLARIPC K EIYDGQEL ...String:
MDKFRMVFQF LQSNQESFMS GICGIMALAS AQLYSAFDFN CPCLPRYNLA YGLGVLLVPP LILFLLGFVL NNNVSMLAEE WRRPQGQRQ KDAAVLRYMF CSMVQRAMIA PAVWVSVTLL DGKCITCAFC TSLPVEALGN ASHHGLPQGE VKRVLARIPC K EIYDGQEL IANEVAVRYL RCISQALGWC FVLLMTTLAF LVRSLRPCFT QAVFLKSRYW SHYIDIERKL FDETCAEHAK SF AKVCIQQ FFQGMSKDLT ATHCHPPRKA PTDAGEASEK LLGITDWDTM NIALGSAWSH PQFEK

UniProtKB: Calcium homeostasis modulator 1

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Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 8 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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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 / Chamber humidity: 85 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV

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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: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 188439
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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