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- EMDB-0919: Cryo-EM structure of the killifish CALHM1 -

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Basic information

Entry
Database: EMDB / ID: EMD-0919
TitleCryo-EM structure of the killifish CALHM1
Map data
Sample
  • Complex: CALHM1
    • Protein or peptide: Calcium homeostasis modulator 1
  • Ligand: CHOLESTEROL HEMISUCCINATE
Keywordschannel / MEMBRANE PROTEIN
Function / homologyCalcium homeostasis modulator family / Calcium homeostasis modulator / ATP export / monoatomic cation channel activity / calcium channel activity / basolateral plasma membrane / endoplasmic reticulum membrane / plasma membrane / Calcium homeostasis modulator 1
Function and homology information
Biological speciesOryzias latipes (Japanese medaka)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsDemura K / Kusakizako T
CitationJournal: Sci Adv / Year: 2020
Title: Cryo-EM structures of calcium homeostasis modulator channels in diverse oligomeric assemblies.
Authors: Kanae Demura / Tsukasa Kusakizako / Wataru Shihoya / Masahiro Hiraizumi / Kengo Nomura / Hiroto Shimada / Keitaro Yamashita / Tomohiro Nishizawa / Akiyuki Taruno / Osamu Nureki /
Abstract: Calcium homeostasis modulator (CALHM) family proteins are Ca-regulated adenosine triphosphate (ATP)-release channels involved in neural functions including neurotransmission in gustation. Here, we ...Calcium homeostasis modulator (CALHM) family proteins are Ca-regulated adenosine triphosphate (ATP)-release channels involved in neural functions including neurotransmission in gustation. Here, we present the cryo-electron microscopy (EM) structures of killifish CALHM1, human CALHM2, and CLHM-1 at resolutions of 2.66, 3.4, and 3.6 Å, respectively. The CALHM1 octamer structure reveals that the N-terminal helix forms the constriction site at the channel pore in the open state and modulates the ATP conductance. The CALHM2 undecamer and CLHM-1 nonamer structures show the different oligomeric stoichiometries among CALHM homologs. We further report the cryo-EM structures of the chimeric construct, revealing that the intersubunit interactions at the transmembrane domain (TMD) and the TMD-intracellular domain linker define the oligomeric stoichiometry. These findings advance our understanding of the ATP conduction and oligomerization mechanisms of CALHM channels.
History
DepositionDec 26, 2019-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lmt
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0919.png

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Map

FileDownload / File: emd_0919.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 368 pix.
= 305.44 Å		0.83 Å/pix.
x 368 pix.
= 305.44 Å		0.83 Å/pix.
x 368 pix.
= 305.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.07997139 - 0.14775826
Average (Standard dev.)0.00012443731 (±0.002646561)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 305.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z305.440305.440305.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0800.1480.000

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Supplemental data

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Mask #1

Fileemd_0919_msk_1.map
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Half map: half map 1

Fileemd_0919_half_map_1.map
Annotationhalf map 1
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Half map: half map 2

Fileemd_0919_half_map_2.map
Annotationhalf map 2
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Sample components

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Entire : CALHM1

EntireName: CALHM1
Components
  • Complex: CALHM1
    • Protein or peptide: Calcium homeostasis modulator 1
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: CALHM1

SupramoleculeName: CALHM1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryzias latipes (Japanese medaka)

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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: Oryzias latipes (Japanese medaka)
Molecular weightTheoretical: 35.039684 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDKFRMMFQF LQSNQESFMN GICGIMALAS AQMYSSFEFS CPCMPEYNYT YGIGLLIIPP IWFFLLGFVL NNNVSVLAEE WKRPTGRRT KDPSVLRYML CSITQRSLIA PAVWVSVTLM DGKSFLCAFS INLDIEKFGN ASLVIGMTET EKLKFLARIP C KDLFEDNE ...String:
MDKFRMMFQF LQSNQESFMN GICGIMALAS AQMYSSFEFS CPCMPEYNYT YGIGLLIIPP IWFFLLGFVL NNNVSVLAEE WKRPTGRRT KDPSVLRYML CSITQRSLIA PAVWVSVTLM DGKSFLCAFS INLDIEKFGN ASLVIGMTET EKLKFLARIP C KDLFEDNE VRVAATRYIK CISQACGWMF LLMMTFTAFL IRAIRPCFTQ AAFLKTKYWS HYIDIERKMF DETCKEHAKS FA KVCIHQY FENISGEMQN FHRHQSKDTS DAEEEEKQRS DEDKLLGIKA QEDMNKVLEN LYFQ

UniProtKB: Calcium homeostasis modulator 1

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 32 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102109
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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