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- EMDB-35631: Cryo-EM structure of hMRS-highEDTA -

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Basic information

Entry
Database: EMDB / ID: EMD-35631
TitleCryo-EM structure of hMRS-highEDTA
Map data
Sample
  • Complex: human MRS2
    • Protein or peptide: Magnesium transporter MRS2 homolog, mitochondrial
  • Ligand: MAGNESIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: water
Keywordspentamer / METAL TRANSPORT
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLi M / Li Y / Yang X / Shen YQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) 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_35631.png

Downloads & links

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Map

FileDownload / File: emd_35631.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 260 pix.
= 241.8 Å		0.93 Å/pix.
x 260 pix.
= 241.8 Å		0.93 Å/pix.
x 260 pix.
= 241.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.27698553 - 0.7513227
Average (Standard dev.)0.00043562 (±0.02451552)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 241.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35631_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_35631_half_map_2.map
Projections & Slices
AxesZYX

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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: MAGNESIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: water

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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)
Molecular weightTheoretical: 250 KDa

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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: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 6.8
GridModel: Quantifoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 1708 / Average electron dose: 51.39 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 374846
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171385
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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