+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21143 | |||||||||
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Title | Cryo-EM structure of octameric chicken CALHM1 | |||||||||
Map data | sharpened map of chicken calcium homeostasis modulator protein 1 | |||||||||
Sample |
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Function / homology | Function and homology information voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / monoatomic cation channel activity / serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.63 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_21143.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-21143-v30.xml emd-21143.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
Images | emd_21143.png | 105 KB | ||
Others | emd_21143_additional.map.gz emd_21143_additional_1.map.gz | 58.5 MB 58.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21143 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21143 | HTTPS FTP |
-Validation report
Summary document | emd_21143_validation.pdf.gz | 523.7 KB | Display | EMDB validaton report |
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Full document | emd_21143_full_validation.pdf.gz | 523.2 KB | Display | |
Data in XML | emd_21143_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_21143_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21143 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21143 | HTTPS FTP |
-Related structure data
Related structure data | 6vamMC 6vaiC 6vakC 6valC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10485 (Title: Chicken CALHM1, 1 mM EDTA / Data size: 2.4 TB Data #1: Unaligned movies (.tif) for chicken CALHM1 in nanodisc [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21143.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map of chicken calcium homeostasis modulator protein 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 of chicken calcium homeostasis modulator protein 1
File | emd_21143_additional.map | ||||||||||||
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Annotation | unsharpened map of chicken calcium homeostasis modulator protein 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map of chicken calcium homeostasis modulator protein 1
File | emd_21143_additional_1.map | ||||||||||||
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Annotation | unsharpened map of chicken calcium homeostasis modulator protein 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Octameric chicken CALHM1 in EDTA
Entire | Name: Octameric chicken CALHM1 in EDTA |
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Components |
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-Supramolecule #1: Octameric chicken CALHM1 in EDTA
Supramolecule | Name: Octameric chicken CALHM1 in EDTA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Gallus gallus (chicken) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Green fluorescent protein,CALHM1 chimera
Macromolecule | Name: Green fluorescent protein,CALHM1 chimera / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 71.65782 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MWSHPQFEKG GGSGGGSGGS AWSHPQFEKG AHHHHHHHHA AAMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKF ICTTGKLPVP WPTLVTTLTY GVQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY KTRAEVKFEG D TLVNRIEL ...String: MWSHPQFEKG GGSGGGSGGS AWSHPQFEKG AHHHHHHHHA AAMVSKGEEL FTGVVPILVE LDGDVNGHKF SVSGEGEGDA TYGKLTLKF ICTTGKLPVP WPTLVTTLTY GVQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGNY KTRAEVKFEG D TLVNRIEL KGIDFKEDGN ILGHKLEYNY NSHNVYIMAD KQKNGIKVNF KIRHNIEDGS VQLADHYQQN TPIGDGPVLL PD NHYLSTQ SKLSKDPNEK RDHMVLLEFV TAAGITLGMD ELYKSGLRSG LEVLFQGPEF DKFRMVFQFL QSNQESFMSG ICG IMALAS AQLYSAFDFN CPCLPRYNLA YGLGVLLVPP LILFLLGFVL NNNVSMLAEE WRRPQGQRQK DAAVLRYMFC SMVQ RAMIA PAVWVSVTLL DGKCITCAFC TSLPVEALGN ASHHGLPQGE VKRVLARIPC KEIYDGQELI ANEVAVRYLR CISQA LGWC FVLLMTTLAF LVRSLRPCFT QAVFLKSRYW SHYIDIERKL FDETCAEHAK SFAKVCIQQF FQGMSKDLTA THCHPP RKA PTDAGEASEK LLGITDWDTM NIALKSWHRC KPPLHLHPDA PHSSNGWAGE WQPHTQPHTQ PPAPRREAVA YYSGV |
-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 |
-Image processing
Final reconstruction | Applied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 308916 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |