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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21140 | |||||||||
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Title | Cryo-EM structure of a dimer of undecameric human CALHM2 | |||||||||
![]() | Dimer of undecameric human calcium homeostasis modulator protein 2, sharpened map | |||||||||
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Function / homology | Calcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic cation channel activity / positive regulation of apoptotic process / membrane / Calcium homeostasis modulator protein 2![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.68 Å | |||||||||
![]() | Syrjanen JL / Chou TH / Furukawa H | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and assembly of calcium homeostasis modulator proteins. Authors: Johanna L Syrjanen / Kevin Michalski / Tsung-Han Chou / Timothy Grant / Shanlin Rao / Noriko Simorowski / Stephen J Tucker / Nikolaus Grigorieff / Hiro Furukawa / ![]() ![]() Abstract: The biological membranes of many cell types contain large-pore channels through which a wide variety of ions and metabolites permeate. Examples include connexin, innexin and pannexin, which form gap ...The biological membranes of many cell types contain large-pore channels through which a wide variety of ions and metabolites permeate. Examples include connexin, innexin and pannexin, which form gap junctions and/or bona fide cell surface channels. The most recently identified large-pore channels are the calcium homeostasis modulators (CALHMs), through which ions and ATP permeate in a voltage-dependent manner to control neuronal excitability, taste signaling and pathologies of depression and Alzheimer's disease. Despite such critical biological roles, the structures and patterns of their oligomeric assembly remain unclear. Here, we reveal the structures of two CALHMs, chicken CALHM1 and human CALHM2, by single-particle cryo-electron microscopy (cryo-EM), which show novel assembly of the four transmembrane helices into channels of octamers and undecamers, respectively. Furthermore, molecular dynamics simulations suggest that lipids can favorably assemble into a bilayer within the larger CALHM2 pore, but not within CALHM1, demonstrating the potential correlation between pore size, lipid accommodation and channel activity. | |||||||||
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 | ![]() | 120.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.3 KB 13.3 KB | Display Display | ![]() |
Images | ![]() | 156.4 KB | ||
Others | ![]() | 119.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 581.3 KB | Display | ![]() |
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Full document | ![]() | 580.8 KB | Display | |
Data in XML | ![]() | 7 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vaiMC ![]() 6vakC ![]() 6valC ![]() 6vamC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 216.5 Data #1: Unaligned movies (.tif) for human CALHM2 gap junction in nanodisc at 1 mM CaCl2 and 1 mM ATP [micrographs - multiframe]) ![]() Data #1: Unaligned movies (.tif) for human CALHM2 in nanodisc at 1 mM EDTA [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Dimer of undecameric human calcium homeostasis modulator protein 2, sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: unsharpened map
File | emd_21140_additional.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Dimer of calcium homeostasis modulator protein 2 (CALHM2) undecam...
Entire | Name: Dimer of calcium homeostasis modulator protein 2 (CALHM2) undecamers (22-mer; gap junction like) |
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Components |
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-Supramolecule #1: Dimer of calcium homeostasis modulator protein 2 (CALHM2) undecam...
Supramolecule | Name: Dimer of calcium homeostasis modulator protein 2 (CALHM2) undecamers (22-mer; gap junction like) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Calcium homeostasis modulator protein 2
Macromolecule | Name: Calcium homeostasis modulator protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 39.514957 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGGTGAALIA ENFRFLSLFF KSKDVMIFNG LVALGTVGSQ ELFSVVAFHC PCSPARNYL YGLAAIGVPA LVLFIIGIIL NNHTWNLVAE CQHRRTKNCS AAPTFLLLSS ILGRAAVAPV TWSVISLLRG E AYVCALSE ...String: MSAWSHPQFE KGGGSGGGSG GSAWSHPQFE KGGTGAALIA ENFRFLSLFF KSKDVMIFNG LVALGTVGSQ ELFSVVAFHC PCSPARNYL YGLAAIGVPA LVLFIIGIIL NNHTWNLVAE CQHRRTKNCS AAPTFLLLSS ILGRAAVAPV TWSVISLLRG E AYVCALSE FVDPSSLTAR EEHFPSAHAT EILARFPCKE NPDNLSDFRE EVSRRLRYES QLFGWLLIGV VAILVFLTKC LK HYCSPLS YRQEAYWAQY RANEDQLFQR TAEVHSRVLA ANNVRRFFGF VALNKDDEEL IANFPVEGTQ PRPQWNAITG VYL YRENQG LPLYSRLHKW AQGLAGNGAA PDNVEMALLP S |
-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: 7.5 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 288.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4 sec before plunging. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: undecameric human CALHM2 |
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Final reconstruction | Applied symmetry - Point group: D11 (2x11 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 52737 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |