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- EMDB-41589: Cryo-EM structure of human MRS2 with Ca2+ -

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Basic information

Entry
Database: EMDB / ID: EMD-41589
TitleCryo-EM structure of human MRS2 with Ca2+
Map data
Sample
  • Complex: hMRS2-BRIL with Ca2+
    • Protein or peptide: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein
  • Ligand: CALCIUM 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 / mitochondrial inner membrane / periplasmic space / electron transfer activity / 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 / mitochondrial inner membrane / periplasmic space / electron transfer activity / iron ion binding / heme binding / mitochondrion
Similarity search - Function
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: 3.11 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: To Be Published
Title: Human mitochondrial MRS2 is a Ca2+-regulated nonselective cation channel
Authors: He Z / Tu Y / Tsai C / Mount JW / Zhang J / Tsai M / Yuan P
History
DepositionAug 10, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_41589.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.5335289 - 1.5929663
Average (Standard dev.)0.005008688 (±0.049853742)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : hMRS2-BRIL with Ca2+

EntireName: hMRS2-BRIL with Ca2+
Components
  • Complex: hMRS2-BRIL with Ca2+
    • Protein or peptide: Magnesium transporter MRS2 homolog, mitochondrial, Soluble cytochrome b562 fusion protein
  • Ligand: CALCIUM ION

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Supramolecule #1: hMRS2-BRIL with Ca2+

SupramoleculeName: hMRS2-BRIL with Ca2+ / 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: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 7 / Formula: CA
Molecular weightTheoretical: 40.078 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 mMGDNglyco-diosgenin
10.0 mMCaCl2Calcium chloride

Details: 20 mM Tris pH 8.0, 150 mM NaCl, 10 mM Ca2+ and 0.04 mM GDN
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 10816 / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 582296
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8ts1

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 125279
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8ts3:
Cryo-EM structure of human MRS2 with Ca2+

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