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Yorodumi- EMDB-21142: Cryo-EM structure of an undecameric chicken CALHM1 and human CALH... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21142 | |||||||||
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Title | Cryo-EM structure of an undecameric chicken CALHM1 and human CALHM2 chimera | |||||||||
Map data | sharpened map of a chicken CALHM1 and human CALHM2 chimera | |||||||||
Sample |
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Function / homology | Function and homology information regulation of microglial cell activation / ATP export / voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / calcium ion import / monoatomic cation channel activity / regulation of synaptic plasticity / serine-type endopeptidase inhibitor activity / positive regulation of apoptotic process / extracellular space ...regulation of microglial cell activation / ATP export / voltage-gated monoatomic ion channel activity / calcium-activated cation channel activity / calcium ion import / monoatomic cation channel activity / regulation of synaptic plasticity / serine-type endopeptidase inhibitor activity / positive regulation of apoptotic process / extracellular space / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.87 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_21142.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-21142-v30.xml emd-21142.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_21142.png | 130.7 KB | ||
Others | emd_21142_additional.map.gz | 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21142 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21142 | HTTPS FTP |
-Validation report
Summary document | emd_21142_validation.pdf.gz | 513.4 KB | Display | EMDB validaton report |
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Full document | emd_21142_full_validation.pdf.gz | 513 KB | Display | |
Data in XML | emd_21142_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_21142_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21142 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21142 | HTTPS FTP |
-Related structure data
Related structure data | 6valMC 6vaiC 6vakC 6vamC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10486 (Title: Chicken CALHM1 - Human CALHM2 chimera / Data size: 1.1 TB Data #1: Unaligned movies (.tif) for chicken CALHM1 - human CALHM2 chimera 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_21142.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map of a chicken CALHM1 and human CALHM2 chimera | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 a chicken CALHM1 and human CALHM2 chimera
File | emd_21142_additional.map | ||||||||||||
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Annotation | unsharpened map of a chicken CALHM1 and human CALHM2 chimera | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : chimera of chicken CALHM1 and human CALHM2
Entire | Name: chimera of chicken CALHM1 and human CALHM2 |
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Components |
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-Supramolecule #1: chimera of chicken CALHM1 and human CALHM2
Supramolecule | Name: chimera of chicken CALHM1 and human CALHM2 / 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: Green fluorescent protein, CALHM1,CALMH2 chimera
Macromolecule | Name: Green fluorescent protein, CALHM1,CALMH2 chimera / 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: 69.023617 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 LVPRGSEFDK FRMVFQFLQS NQESFMSGIC GIM ALASAQ LYSAFDFNCP CLPRYNLAYG LGVLLVPPLI LFLLGFVLNN NVSMLAEEWR RPQGQRQKDA AVLRYMFCSM VQRA MIAPA VWVSVTLLDG KCITCAFCTS LPVEALGNAS HHGLPQGEVK RVLARIPCKE IYDGQELIAN EVAVRYLRCI SQALG WCFV LLMTTLAFLV RSLKHYCSPL SYRQEAYWAQ YRANEDQLFQ RTAEVHSRVL AANNVRRFFG FVALNKDDEE LIANFP VEG TQPRPQWNAI TGVYLYRENQ GLPLYSRLHK WAQGLAGNGA APDNVEMALL PS |
-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: 57.2 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
Startup model | Type of model: OTHER Details: undecameric human CALHM2 and octameric chicken CALHM1 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 123664 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |