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- PDB-8ts2: Cryo-EM structure of human MRS2 with EDTA -

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Basic information

Entry
Database: PDB / ID: 8ts2
TitleCryo-EM structure of human MRS2 with EDTA
ComponentsMagnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein
KeywordsMETAL TRANSPORT / mitochondria / pentamer / cation channel
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsHe, Z. / Mount, J.W. / Zhang, J. / Yuan, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS109307 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin / pdbx_entry_details
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Revision 1.2Dec 11, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.3Apr 2, 2025Group: Data collection / Database references / Category: citation / em_admin
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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, Soluble cytochrome b562 fusion protein
B: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein
C: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein
D: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein
E: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein


Theoretical massNumber of molelcules
Total (without water)277,3585
Polymers277,3585
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 82 - 399 / Label seq-ID: 22 - 339

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE

NCS oper:
IDCodeMatrixVector
1given(0.309017090654, 0.951056485012, -3.35060975339E-8), (-0.951056485012, 0.309017090654, -8.71191383482E-8), (-7.25012647156E-8, 5.87874940197E-8, 1)-37.4505937068, 236.453689704, 2.54310208447E-7
2given(-0.809016855507, 0.587785443428, 1.91951391398E-8), (-0.587785443428, -0.809016855507, -1.12695733932E-8), (8.90509991373E-9, -2.03998982004E-8, 1)175.857324878, 345.13952782, 2.00101970904E-6
3given(-0.80945885899, -0.587165125769, -0.00367024288707), (0.587173378946, -0.809459303215, -0.00174914134536), (-0.00194387745196, -0.00357092687518, 0.999991734877)345.579393647, 176.22288686, 0.800501862624
4given(0.30901731385, -0.951056412491, -3.76714979551E-8), (0.951056412491, 0.30901731385, -3.53109203292E-8), (4.52238223169E-8, -2.49160339487E-8, 1)236.453632498, -37.4506080266, -1.97105046595E-6

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Components

#1: Protein
Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein / Cytochrome b-562


Mass: 55471.691 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: hMRS2-dNdC-BRIL,hMRS2-dNdC-BRIL / Source: (gene. exp.) Homo sapiens (human) / Gene: MRS2, cybC / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9HD23, UniProt: P0ABE7
Has protein modificationN

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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: hMRS2-BRIL with EDTA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 8
Details: 20 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA and 0.04 mM GDN
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisTris1
2150 mMsodium chlorideNaCl1
30.04 mMglyco-diosgeninGDN1
410 mMEthylenediaminetetraacetic acidEDTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 3477

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Processing

EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1249448
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 406358 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 114.31 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412445
ELECTRON MICROSCOPYf_angle_d0.440216790
ELECTRON MICROSCOPYf_chiral_restr0.03361955
ELECTRON MICROSCOPYf_plane_restr0.00242105
ELECTRON MICROSCOPYf_dihedral_angle_d3.43231615
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints1.68791548111E-11
ens_1d_3AAELECTRON MICROSCOPYNCS constraints1.2100773181E-9
ens_1d_4AAELECTRON MICROSCOPYNCS constraints1.02022041107E-12
ens_1d_5AAELECTRON MICROSCOPYNCS constraints4.80719792198E-10

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