+Open data
-Basic information
Entry | Database: PDB / ID: 6vai | |||||||||
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Title | Cryo-EM structure of a dimer of undecameric human CALHM2 | |||||||||
Components | Calcium homeostasis modulator protein 2 | |||||||||
Keywords | MEMBRANE PROTEIN / taste / assembly / calcium / gap junction | |||||||||
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) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å | |||||||||
Authors | Syrjanen, J.L. / Chou, T.H. / Furukawa, H. | |||||||||
Funding support | United States, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6vai.cif.gz | 983.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vai.ent.gz | 834.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vai_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6vai_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6vai_validation.xml.gz | 145.3 KB | Display | |
Data in CIF | 6vai_validation.cif.gz | 191.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/6vai ftp://data.pdbj.org/pub/pdb/validation_reports/va/6vai | HTTPS FTP |
-Related structure data
Related structure data | 21140MC 6vakC 6valC 6vamC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10487 (Title: Human CALHM2 gap junction in nanodisc, 1 mM CaCl2 and 1 mM ATP Data size: 216.5 Data #1: Unaligned movies (.tif) for human CALHM2 gap junction in nanodisc at 1 mM CaCl2 and 1 mM ATP [micrographs - multiframe]) EMPIAR-10488 (Title: Human CALHM2 in nanodisc, 1 mM EDTA / Data size: 604.3 Data #1: Unaligned movies (.tif) for human CALHM2 in nanodisc at 1 mM EDTA [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 39514.957 Da / Num. of mol.: 22 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALHM2, FAM26B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9HA72 |
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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: Dimer of calcium homeostasis modulator protein 2 (CALHM2) undecamers (22-mer; gap junction like) Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 288.15 K / Details: Blot for 4 sec before plunging |
-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 |
Image recording | Electron dose: 70 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Symmetry | Point symmetry: D11 (2x11 fold dihedral) | ||||||||||||
3D reconstruction | Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52737 / Symmetry type: POINT |