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- EMDB-41587: Cryo-EM structure of human MRS2 with Mg2+ -

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Basic information

Entry
Database: EMDB / ID: EMD-41587
TitleCryo-EM structure of human MRS2 with Mg2+
Map data
Sample
  • Complex: hMRS2-BRIL with Mg2+
    • Protein or peptide: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein
  • Ligand: MAGNESIUM ION
Keywordsmitochondria / pentamer / cation channel / 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 / electron transport chain / transmembrane transport / periplasmic space / electron transfer activity / mitochondrial inner membrane / iron ion binding ...mitochondrial magnesium ion transmembrane transport / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity / lactate metabolic process / electron transport chain / transmembrane transport / periplasmic space / electron transfer activity / mitochondrial inner membrane / iron ion binding / heme binding / mitochondrion
Similarity search - Function
Magnesium transporter MRS2-like / Magnesium transporter MRS2-like / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Soluble cytochrome b562 / Magnesium transporter MRS2 homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsHe Z / Mount JW / Zhang J / Yuan P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS109307 United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structure and function of the human mitochondrial MRS2 channel.
Authors: Zhihui He / Yung-Chi Tu / Chen-Wei Tsai / Jonathan Mount / Jingying Zhang / Ming-Feng Tsai / Peng Yuan /
Abstract: The human mitochondrial RNA splicing 2 protein (MRS2) has been implicated in Mg transport across mitochondrial inner membranes, thus having an important role in Mg homeostasis critical for ...The human mitochondrial RNA splicing 2 protein (MRS2) has been implicated in Mg transport across mitochondrial inner membranes, thus having an important role in Mg homeostasis critical for mitochondrial integrity and function. However, the molecular mechanisms underlying its fundamental channel properties such as ion selectivity and regulation remain unclear. Here we present a structural and functional investigation of MRS2. Cryo-electron microscopy structures in various ionic conditions reveal a pentameric channel architecture and the molecular basis of ion permeation and potential regulation mechanisms. Electrophysiological analyses demonstrate that MRS2 is a Ca-regulated, nonselective channel permeable to Mg, Ca, Na and K, which contrasts with its prokaryotic ortholog, CorA, operating as a Mg-gated Mg channel. Moreover, a conserved arginine ring within the pore of MRS2 functions to restrict cation movements, thus preventing the channel from collapsing the proton motive force that drives mitochondrial adenosine triphosphate synthesis. Together, our results provide a molecular framework for further understanding MRS2 in mitochondrial function and disease.
History
DepositionAug 10, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41587.png

Downloads & links

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Map

FileDownload / File: emd_41587.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 240 pix.
= 288. Å		1.2 Å/pix.
x 240 pix.
= 288. Å		1.2 Å/pix.
x 240 pix.
= 288. Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-4.009814 - 7.0693603
Average (Standard dev.)0.0017984902 (±0.15669112)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_41587_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_41587_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_41587_half_map_2.map
Projections & Slices
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Sample components

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Entire : hMRS2-BRIL with Mg2+

EntireName: hMRS2-BRIL with Mg2+
Components
  • Complex: hMRS2-BRIL with Mg2+
    • Protein or peptide: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein
  • Ligand: MAGNESIUM ION

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Supramolecule #1: hMRS2-BRIL with Mg2+

SupramoleculeName: hMRS2-BRIL with Mg2+ / 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, Soluble cytoch...

MacromoleculeName: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein
type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 55.471691 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MVAGEVHRFR TSDVSQATLA SVAPVFTVTK FDKQGNVTSF ERKKTELYQE LGLQARDLRF QHVMSITVRN NRIIMRMEYL KAVITPECL LILDYRNLNL EQWLFRELPS QLSGEGQLVT YPLPFEFRAI EALLQYWINT LQGKLSILQP LILETLDALV D PKHSSVDR ...String:
MVAGEVHRFR TSDVSQATLA SVAPVFTVTK FDKQGNVTSF ERKKTELYQE LGLQARDLRF QHVMSITVRN NRIIMRMEYL KAVITPECL LILDYRNLNL EQWLFRELPS QLSGEGQLVT YPLPFEFRAI EALLQYWINT LQGKLSILQP LILETLDALV D PKHSSVDR SKLHILLQNG KSLSELETDI KIFKESILEI LDEEELLEEL CVSKWSDPQV FEKSSAGIDH AEEMELLLEN YY RLADDLS NAARELRVLI DDSQSIIFIN LDSHRNVMMR LNLQLTMGTF SLSLFGLMGV AFGMNLESSL EEDHRIFWLI TGI MFMGSG LIWRRLLSFL GRQLEAPLPP MMASLPKKTL LADRSMELKN SLRLDADLED NWETLNDNLK VIEKADNAAQ VKDA LTKMR AAALDAQKAT PPKLEDKSPD SPEMKDFRHG FDILVGQIDD ALKLANEGKV KEAQAAAEQL KTTRNAYIQK YLSNS LEVL FQ

UniProtKB: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 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

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris
150.0 mMNaClsodium chloride
0.04 mMGDNGDN
40.0 mMMgCl2Magnesium chloride

Details: 20 mM Tris pH 8.0, 150 mM NaCl, 40 mM MgCl2 and 0.04 mM GDN
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 2631 / Average electron dose: 41.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000

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Image processing

Particle selectionNumber selected: 937963
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 719778
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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