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Yorodumi- EMDB-19362: Cryo-EM structure of human CALHM2 in complex with synthetic nanob... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19362 | |||||||||
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Title | Cryo-EM structure of human CALHM2 in complex with synthetic nanobody SbC2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ion channel / large pore channels / sybody / CALHM / MEMBRANE PROTEIN | |||||||||
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) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.07 Å | |||||||||
Authors | 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_19362.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-19362-v30.xml emd-19362.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19362_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_19362.png | 43.4 KB | ||
Filedesc metadata | emd-19362.cif.gz | 5.6 KB | ||
Others | emd_19362_half_map_1.map.gz emd_19362_half_map_2.map.gz | 59 MB 59 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19362 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19362 | HTTPS FTP |
-Validation report
Summary document | emd_19362_validation.pdf.gz | 886.8 KB | Display | EMDB validaton report |
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Full document | emd_19362_full_validation.pdf.gz | 886.4 KB | Display | |
Data in XML | emd_19362_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_19362_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19362 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19362 | HTTPS FTP |
-Related structure data
Related structure data | 8rmkMC 8rmlC 8rmmC 8rmnC 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_19362.map.gz / Format: CCP4 / Size: 64 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: 1.31 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_19362_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19362_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of CALHM2 channel with synthetic nanobody SbC2
Entire | Name: Complex of CALHM2 channel with synthetic nanobody SbC2 |
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Components |
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-Supramolecule #1: Complex of CALHM2 channel with synthetic nanobody SbC2
Supramolecule | Name: Complex of CALHM2 channel with synthetic nanobody SbC2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 590 KDa |
-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: 37.099535 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSAALIAENF RFLSLFFKSK DVMIFNGLVA LGTVGSQELF SVVAFHCPCS PARNYLYGLA AIGVPALVLF IIGIILNNHT WNLVAECQH RRTKNCSAAP TFLLLSSILG RAAVAPVTWS VISLLRGEAY VCALSEFVDP SSLTAREEHF PSAHATEILA R FPCKENPD ...String: MSAALIAENF RFLSLFFKSK DVMIFNGLVA LGTVGSQELF SVVAFHCPCS PARNYLYGLA AIGVPALVLF IIGIILNNHT WNLVAECQH RRTKNCSAAP TFLLLSSILG RAAVAPVTWS VISLLRGEAY VCALSEFVDP SSLTAREEHF PSAHATEILA R FPCKENPD NLSDFREEVS RRLRYESQLF GWLLIGVVAI LVFLTKCLKH YCSPLSYRQE AYWAQYRANE DQLFQRTAEV HS RVLAANN VRRFFGFVAL NKDDEELIAN FPVEGTQPRP QWNAITGVYL YRENQGLPLY SRLHKWAQGL AGNGAAPDNV EMA LLPSAL EVLFQ UniProtKB: Calcium homeostasis modulator protein 2 |
-Macromolecule #2: Synthetic nanobody SbC2
Macromolecule | Name: Synthetic nanobody SbC2 / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 16.80334 KDa |
Recombinant expression | Organism: Escherichia coli MC1061 (bacteria) |
Sequence | String: SSSQVQLVES GGGSVQAGGS LRLSCAASGN IRNISYLGWF RQAPGKEREG VAALWTTQGQ TYYADSVKGR FTVSLDNAKN TVYLQMNSL KPEDTALYYC AAATSGQYNP LRGYHYNEYW GQGTQVTVSA GRAGEQKLIS EEDLNSAVDH HHHHH |
-Macromolecule #3: DIUNDECYL PHOSPHATIDYL CHOLINE
Macromolecule | Name: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 3 / Number of copies: 11 / Formula: PLC |
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Molecular weight | Theoretical: 622.834 Da |
Chemical component information | ChemComp-PLC: |
-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: 72.0 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 / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |