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Yorodumi- EMDB-19365: Cryo-EM structure of a dimer of decameric human CALHM4 in complex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19365 | |||||||||
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Title | Cryo-EM structure of a dimer of decameric human CALHM4 in complex with synthetic nanobody SbC4 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ion channel / large pore channels / sybody / CALHM / MEMBRANE PROTEIN | |||||||||
Function / homology | Calcium homeostasis modulator family / Calcium homeostasis modulator / monoatomic cation channel activity / plasma membrane / Calcium homeostasis modulator protein 4 Function and homology information | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Peter M / Drozdzyk K / Dutzler R | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: Elife / Year: 2024 Title: Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs. Authors: Katarzyna Drożdżyk / Martina Peter / Raimund Dutzler / Abstract: The CALHM proteins constitute a family of large pore channels that contains six closely related paralogs in humans. Two family members, CALHM1 and 3, have been associated with the release of ATP ...The CALHM proteins constitute a family of large pore channels that contains six closely related paralogs in humans. Two family members, CALHM1 and 3, have been associated with the release of ATP during taste sensation. Both proteins form heteromeric channels that activate at positive potential and decreased extracellular Ca concentration. Although the structures of several family members displayed large oligomeric organizations of different size, their function has in most cases remained elusive. Our previous study has identified the paralogs CALHM2, 4 and, 6 to be highly expressed in the placenta and defined their structural properties as membrane proteins exhibiting features of large pore channels with unknown activation properties (Drożdżyk et al., 2020). Here, we investigated whether these placental paralogs would form heteromers and characterized heteromeric complexes consisting of CALHM2 and CALHM4 subunits using specific binders as fiducial markers. Both proteins assemble with different stoichiometries with the largest population containing CALHM2 as the predominant component. In these oligomers, the subunits segregate and reside in their preferred conformation found in homomeric channels. Our study has thus revealed the properties that govern the formation of CALHM heteromers in a process of potential relevance in a cellular context. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19365.map.gz | 432.9 MB | EMDB map data format | |
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Header (meta data) | emd-19365-v30.xml emd-19365.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19365_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_19365.png | 52.5 KB | ||
Filedesc metadata | emd-19365.cif.gz | 5.5 KB | ||
Others | emd_19365_half_map_1.map.gz emd_19365_half_map_2.map.gz | 378 MB 378 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19365 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19365 | HTTPS FTP |
-Validation report
Summary document | emd_19365_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_19365_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_19365_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | emd_19365_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19365 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19365 | HTTPS FTP |
-Related structure data
Related structure data | 8rmnMC 8rmkC 8rmlC 8rmmC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19365.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.651 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_19365_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19365_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of CALHM4 channel with synthetic nanobody SbC4
Entire | Name: Complex of CALHM4 channel with synthetic nanobody SbC4 |
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Components |
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-Supramolecule #1: Complex of CALHM4 channel with synthetic nanobody SbC4
Supramolecule | Name: Complex of CALHM4 channel with synthetic nanobody SbC4 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.03 MDa |
-Macromolecule #1: Calcium homeostasis modulator protein 4
Macromolecule | Name: Calcium homeostasis modulator protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 35.981656 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSCPTLNNIV SSLQRNGIFI NSLIAALTIG GQQLFSSSTF SCPCQVGKNF YYGSAFLVIP ALILLVAGFA LRSQMWTITG EYCCSCAPP YRRISPLECK LACLRFFSIT GRAVIAPLTW LAVTLLTGTY YECAASEFAS VDHYPMFDNV SASKREEILA G FPCCRSAP ...String: MSCPTLNNIV SSLQRNGIFI NSLIAALTIG GQQLFSSSTF SCPCQVGKNF YYGSAFLVIP ALILLVAGFA LRSQMWTITG EYCCSCAPP YRRISPLECK LACLRFFSIT GRAVIAPLTW LAVTLLTGTY YECAASEFAS VDHYPMFDNV SASKREEILA G FPCCRSAP SDVILVRDEI ALLHRYQSQM LGWILITLAT IAALVSCCVA KCCSPLTSLQ HCYWTSHLQN ERELFEQAAE QH SRLLMMH RIKKLFGFIP GSEDVKHIRI PSCQDWKDIS VPTLLCMGDD LQGHYSFLGN RVDEDNEEDR SRGIELKPAL EVL FQ UniProtKB: Calcium homeostasis modulator protein 4 |
-Macromolecule #2: Synthetic nanobody SbC4
Macromolecule | Name: Synthetic nanobody SbC4 / type: protein_or_peptide / ID: 2 / Number of copies: 20 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 15.613268 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SSSQVQLVES GGGLVQAGGS LRLSCAASGF PVYYTHMRWY RQAPGKEREW VAAIYSKGAG THYADSVKGR FTISRDNAKN TVYLQMNSL KPEDTAVYYC FVGVGNSYIG QGTQVTVSAG RAGEQKLISE EDLNSAVDHH HHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-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: 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 / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |