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- PDB-8ip6: Cryo-EM structure of hMRS2-rest -

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Basic information

Entry
Database: PDB / ID: 8ip6
TitleCryo-EM structure of hMRS2-rest
ComponentsMagnesium transporter MRS2 homolog, mitochondrial
KeywordsMETAL TRANSPORT / pentamer
Function / homologymitochondrial 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
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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

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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)257,6946
Polymers257,6585
Non-polymers351
Water0
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 / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
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 weightExperimental 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, 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 FIELDBright-field microscopy / 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: 54 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 695

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Processing

EM software
IDNameVersionCategory
1Gautomatchparticle selection
2EPUimage acquisition
13cryoSPARC3.23D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 170283
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104000 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00213155
ELECTRON MICROSCOPYf_angle_d0.42717785
ELECTRON MICROSCOPYf_dihedral_angle_d13.0014935
ELECTRON MICROSCOPYf_chiral_restr0.0362060
ELECTRON MICROSCOPYf_plane_restr0.0032250

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