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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0919 | |||||||||
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Title | Cryo-EM structure of the killifish CALHM1 | |||||||||
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Function / homology | Calcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic cation channel activity / membrane / Calcium homeostasis modulator 1![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.66 Å | |||||||||
![]() | Demura K / Kusakizako T / Shihoya W / Hiraizumi M / Shimada H / Yamashita K / Nishizawa T / Nureki O | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 135.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.8 KB 13.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13 KB | Display | ![]() |
Images | ![]() | 142.6 KB | ||
Masks | ![]() | 190.1 MB | ![]() | |
Others | ![]() ![]() | 145.3 MB 145.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 697.4 KB | Display | ![]() |
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Full document | ![]() | 697 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lmtMC ![]() 0920C ![]() 0921C ![]() 0922C ![]() 0923C ![]() 6lmuC ![]() 6lmvC ![]() 6lmwC ![]() 6lmxC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 6.8 TB Data #1: Unaligned movies for OlCALHM1 [micrographs - multiframe] Data #2: Unaligned movies for HsCALHM2 [micrographs - multiframe] Data #3: Unaligned movies for CeCLHM-1 [micrographs - multiframe] Data #4: Unaligned movies for OlCALHM1-HsCALHM2 chimera [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_0919_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_0919_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : CALHM1
Entire | Name: CALHM1 |
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Components |
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-Supramolecule #1: CALHM1
Supramolecule | Name: CALHM1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Calcium homeostasis modulator 1
Macromolecule | Name: Calcium homeostasis modulator 1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 35.039684 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #2: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 32 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ![]() ChemComp-Y01: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |