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Open data
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Basic information
Entry | Database: PDB / ID: 8ip3 | ||||||
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Title | Cryo-EM structure of hMRS2-Mg | ||||||
![]() | Magnesium transporter MRS2 homolog, mitochondrial | ||||||
![]() | METAL TRANSPORT / pentamer | ||||||
Function / homology | mitochondrial magnesium ion transmembrane transport / Magnesium transporter MRS2-like / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity / lactate metabolic process / transmembrane transport / mitochondrial inner membrane / mitochondrion / Magnesium transporter MRS2 homolog, mitochondrial![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
![]() | Li, M. / Li, Y. / Yang, X. / Shen, Y.Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of Mg permeation through the human mitochondrial Mrs2 channel. Authors: Ming Li / Yang Li / Yue Lu / Jianhui Li / Xuhang Lu / Yue Ren / Tianlei Wen / Yaojie Wang / Shenghai Chang / Xing Zhang / Xue Yang / Yuequan Shen / ![]() Abstract: Mitochondrial RNA splicing 2 (Mrs2), a eukaryotic CorA ortholog, enables Mg to permeate the inner mitochondrial membrane and plays an important role in mitochondrial metabolic function. However, the ...Mitochondrial RNA splicing 2 (Mrs2), a eukaryotic CorA ortholog, enables Mg to permeate the inner mitochondrial membrane and plays an important role in mitochondrial metabolic function. However, the mechanism by which Mrs2 permeates Mg remains unclear. Here, we report four cryo-electron microscopy (cryo-EM) reconstructions of Homo sapiens Mrs2 (hMrs2) under various conditions. All of these hMrs2 structures form symmetrical pentamers with very similar pentamer and protomer conformations. A special structural feature of Cl-bound R-ring, which consists of five Arg332 residues, was found in the hMrs2 structure. Molecular dynamics simulations and mitochondrial Mg uptake assays show that the R-ring may function as a charge repulsion barrier, and Cl may function as a ferry to jointly gate Mg permeation in hMrs2. In addition, the membrane potential is likely to be the driving force for Mg permeation. Our results provide insights into the channel assembly and Mg permeation of hMrs2. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 290.5 KB | Display | ![]() |
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PDB format | ![]() | 233.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 35630MC ![]() 8ip4C ![]() 8ip5C ![]() 8ip6C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 51531.672 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-MG / Has ligand of interest | N | |
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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 |
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Sample preparation
Component | Name: human MRS2 / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.25 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 Details: 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 20 mM MgCl2, 0.007% (w/v) glycol-diosgenin and 1 mM DTT |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 59.97 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3329 |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 473653 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 304325 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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