+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21141 | |||||||||
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Title | Cryo-EM structure of human CALHM2 | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Function / homology | Function and homology information regulation of microglial cell activation / ATP export / calcium ion import / monoatomic cation channel activity / regulation of synaptic plasticity / positive regulation of apoptotic process / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
Authors | Syrjanen JL / Chou TH / Furukawa H | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21141.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-21141-v30.xml emd-21141.xml | 13 KB 13 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21141_fsc.xml | 677 KB | Display | FSC data file |
Images | emd_21141.png | 114 KB | ||
Others | emd_21141_additional.map.gz | 58.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21141 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21141 | HTTPS FTP |
-Validation report
Summary document | emd_21141_validation.pdf.gz | 538.8 KB | Display | EMDB validaton report |
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Full document | emd_21141_full_validation.pdf.gz | 538.3 KB | Display | |
Data in XML | emd_21141_validation.xml.gz | 117.7 KB | Display | |
Data in CIF | emd_21141_validation.cif.gz | 273.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21141 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21141 | HTTPS FTP |
-Related structure data
Related structure data | 6vakMC 6vaiC 6valC 6vamC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21141.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
File | emd_21141_additional.map | ||||||||||||
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Annotation | unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Undecameric assembly of human calcium homeostasis modulator prote...
Entire | Name: Undecameric assembly of human calcium homeostasis modulator protein 2 (CALHM2) in EDTA |
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Components |
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-Supramolecule #1: Undecameric assembly of human calcium homeostasis modulator prote...
Supramolecule | Name: Undecameric assembly of human calcium homeostasis modulator protein 2 (CALHM2) in EDTA type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Calcium homeostasis modulator protein 2
Macromolecule | Name: Calcium homeostasis modulator protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 37.468871 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MAALIAENFR FLSLFFKSKD VMIFNGLVAL GTVGSQELFS VVAFHCPCSP ARNYLYGLAA IGVPALVLFI IGIILNNHTW NLVAECQHR RTKNCSAAPT FLLLSSILGR AAVAPVTWSV ISLLRGEAYV CALSEFVDPS SLTAREEHFP SAHATEILAR F PCKENPDN ...String: MAALIAENFR FLSLFFKSKD VMIFNGLVAL GTVGSQELFS VVAFHCPCSP ARNYLYGLAA IGVPALVLFI IGIILNNHTW NLVAECQHR RTKNCSAAPT FLLLSSILGR AAVAPVTWSV ISLLRGEAYV CALSEFVDPS SLTAREEHFP SAHATEILAR F PCKENPDN LSDFREEVSR RLRYESQLFG WLLIGVVAIL VFLTKCLKHY CSPLSYRQEA YWAQYRANED QLFQRTAEVH SR VLAANNV RRFFGFVALN KDDEELIANF PVEGTQPRPQ WNAITGVYLY RENQGLPLYS RLHKWAQGLA GNGAAPDNVE MAL LPSGSA WSHPQFEK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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. |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |