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- EMDB-35633: Cryo-EM structure of hMRS2-rest -

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Basic information

Entry
Database: EMDB / ID: EMD-35633
TitleCryo-EM structure of hMRS2-rest
Map data
Sample
  • Complex: human MRS2
    • Protein or peptide: Magnesium transporter MRS2 homolog, mitochondrial
  • Ligand: CHLORIDE IONChloride
Keywordspentamer / METAL TRANSPORT
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsLi M / Li Y / Yang X / Shen YQ
Funding support China, 1 items
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, 2023-
Header (metadata) releaseJun 14, 2023-
Map releaseJun 14, 2023-
UpdateAug 30, 2023-
Current statusAug 30, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_35633.png

Downloads & links

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Map

FileDownload / File: emd_35633.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.49616373 - 1.613731
Average (Standard dev.)0.000056877303 (±0.046634547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 263.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35633_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35633_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human MRS2

EntireName: human MRS2
Components
  • Complex: human MRS2
    • Protein or peptide: Magnesium transporter MRS2 homolog, mitochondrial
  • Ligand: CHLORIDE IONChloride

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Supramolecule #1: human MRS2

SupramoleculeName: human MRS2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Magnesium transporter MRS2 homolog, mitochondrial

MacromoleculeName: Magnesium transporter MRS2 homolog, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.531672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MECLRSLPCL LPRAMRLPRR TLCALALDVT SVGPPVAACG RRANLIGRSR AAQLCGPDRL RVAGEVHRFR TSDVSQATLA SVAPVFTVT KFDKQGNVTS FERKKTELYQ ELGLQARDLR FQHVMSITVR NNRIIMRMEY LKAVITPECL LILDYRNLNL E QWLFRELP ...String:
MECLRSLPCL LPRAMRLPRR TLCALALDVT SVGPPVAACG RRANLIGRSR AAQLCGPDRL RVAGEVHRFR TSDVSQATLA SVAPVFTVT KFDKQGNVTS FERKKTELYQ ELGLQARDLR FQHVMSITVR NNRIIMRMEY LKAVITPECL LILDYRNLNL E QWLFRELP SQLSGEGQLV TYPLPFEFRA IEALLQYWIN TLQGKLSILQ PLILETLDAL VDPKHSSVDR SKLHILLQNG KS LSELETD IKIFKESILE ILDEEELLEE LCVSKWSDPQ VFEKSSAGID HAEEMELLLE NYYRLADDLS NAARELRVLI DDS QSIIFI NLDSHRNVMM RLNLQLTMGT FSLSLFGLMG VAFGMNLESS LEEDHRIFWL ITGIMFMGSG LIWRRLLSFL GRQL EAPLP PMMASLPKKT LLADRSMELK NSLRLDGLGS GRSILTNRSA DYKDDDDK

UniProtKB: Magnesium transporter MRS2 homolog, mitochondrial

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Macromolecule #2: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 8
Details: 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.007% (w/v) glycol-diosgenin and 1 mM DTT
GridModel: Quantifoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 695 / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 170283
Startup modelType of model: OTHER
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 104000

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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