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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 / 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)
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: To Be Published
Title: Human mitochondrial MRS2 is a Ca2+-regulated nonselective cation channel
Authors: He, Z. / Tu, Y. / Tsai, C. / Mount, J.W. / Zhang, J. / Tsai, M. / Yuan, P.
History
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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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

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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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