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Yorodumi- PDB-8rmk: Cryo-EM structure of human CALHM2 in complex with synthetic nanob... -
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-Basic information
Entry | Database: PDB / ID: 8rmk | ||||||
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Title | Cryo-EM structure of human CALHM2 in complex with synthetic nanobody SbC2 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / ion channel / large pore channels / sybody / CALHM | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.07 Å | ||||||
Authors | Drozdzyk, K. / Dutzler, R. | ||||||
Funding support | Switzerland, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rmk.cif.gz | 869.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rmk.ent.gz | 723.4 KB | Display | PDB format |
PDBx/mmJSON format | 8rmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rmk_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8rmk_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8rmk_validation.xml.gz | 130.4 KB | Display | |
Data in CIF | 8rmk_validation.cif.gz | 173.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/8rmk ftp://data.pdbj.org/pub/pdb/validation_reports/rm/8rmk | HTTPS FTP |
-Related structure data
Related structure data | 19362MC 8rmlC 8rmmC 8rmnC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 37099.535 Da / Num. of mol.: 11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALHM2, FAM26B / Production host: Homo sapiens (human) / References: UniProt: Q9HA72 #2: Antibody | Mass: 16803.340 Da / Num. of mol.: 11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli MC1061 (bacteria) #3: Chemical | ChemComp-PLC / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of CALHM2 channel with synthetic nanobody SbC2 Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.59 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 72 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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Symmetry | Point symmetry: C11 (11 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37894 / Symmetry type: POINT | ||||||||||||||||||||||||
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