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- PDB-8ip3: Cryo-EM structure of hMRS2-Mg -

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Basic information

Entry
Database: PDB / ID: 8ip3
TitleCryo-EM structure of hMRS2-Mg
ComponentsMagnesium transporter MRS2 homolog, mitochondrial
KeywordsMETAL TRANSPORT / pentamer
Function / homology
Function and homology information


mitochondrial magnesium ion transmembrane transport / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity / lactate metabolic process / transmembrane transport / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Magnesium transporter MRS2-like / Magnesium transporter MRS2-like
Similarity search - Domain/homology
Magnesium transporter MRS2 homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLi, M. / Li, Y. / Yang, X. / Shen, Y.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
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.
History
DepositionMar 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Magnesium transporter MRS2 homolog, mitochondrial
B: Magnesium transporter MRS2 homolog, mitochondrial
C: Magnesium transporter MRS2 homolog, mitochondrial
D: Magnesium transporter MRS2 homolog, mitochondrial
E: Magnesium transporter MRS2 homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,98518
Polymers257,6585
Non-polymers32713
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Magnesium transporter MRS2 homolog, mitochondrial / MRS2-like protein


Mass: 51531.672 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MRS2, HPT, MRS2L / Cell (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: Q9HD23
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human MRS2 / Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.25 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK-293F
Buffer solutionpH: 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
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil
VitrificationInstrument: 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron 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
IDNameVersionCategory
1Gautomatchparticle selection
2EPUimage acquisition
12cryoSPARC3.23D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 473653
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 304325 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00213085
ELECTRON MICROSCOPYf_angle_d0.42517685
ELECTRON MICROSCOPYf_dihedral_angle_d10.7584895
ELECTRON MICROSCOPYf_chiral_restr0.0372050
ELECTRON MICROSCOPYf_plane_restr0.0032235

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