2024-05-01 REL RCSB RCSB RCSB 2023-08-16 2023-09-13 2023-09-13 2024-05-01 National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) ZIA HD008998 United States Lai LTF Balaraman J Zhou F Matthies D Magnesium, Ion channel, Membrane protein, METAL TRANSPORT, Ion Translocation, Divalent Ion, Pentamer Lai LTF Balaraman J Zhou F Matthies D Nat Commun UK 14 7207 7207 2023 37938562 doi:10.1038/s41467-023-42599-3 2041-1723 EMD-41624 other EM volume

Cryo-EM structure of the human MRS2 magnesium channel under Mg2+ condition

8tup FULLOVERLAP Cryo-EM structure of the pentameric human MRS2 magnesium channel under Mg2+-free condition at an average resolution of 3.3 A, filtered to local resolution, C5 Cryo-EM structure of the pentameric human MRS2 magnesium channel under Mg2+-free condition at an average resolution of 3.3 A, filtered to local resolution, C5 0 1 Homo sapiens 0.219 Magnesium transporter MRS2 homolog, mitochondrial Homo sapiens 0.051373516 5 Homo sapiens LEVO MECLRSLPCLLPRAMRLPRRTLCALALDVTSVGPPVAACGRRANLIGRSRAAQLCGPDRLRVAGEVHRFRTSDVSQATLA SVAPVFTVTKFDKQGNVTSFERKKTELYQELGLQARDLRFQHVMSITVRNNRIIMRMEYLKAVITPECLLILDYRNLNLE QWLFRELPSQLSGEGQLVTYPLPFEFRAIEALLQYWINTLQGKLSILQPLILETLDALVDPKHSSVDRSKLHILLQNGKS LSELETDIKIFKESILEILDEEELLEELCVSKWSDPQVFEKSSAGIDHAEEMELLLENYYRLADDLSNAARELRVLIDDS QSIIFINLDSHRNVMMRLNLQLTMGTFSLSLFGLMGVAFGMNLESSLEEDHRIFWLITGIMFMGSGLIWRRLLSFLGRQL EAPLPPMMASLPKKTLLADRSMELKNSLRLDGLGSGRSILTNRDYKDDDDK Q9HD23 MAGNESIUM ION 2.4305e-05 3 MG water 1.8015e-05 66 HOH singleParticle particle 0.5 7.3 20.0 HEPES 150.0 NaCl 1.0 EDTA 0.003 LMNG

20 mM HEPES, 150 mM NaCl, 1mM EDTA, 0.003% LMNG, pH 7.3

Quantifoil R1.2/1.3 COPPER 400 GLOW DISCHARGE 60 AIR ETHANE 95 277 LEICA EM GP

400-mesh R1.2/1.3 Cu grids (Quantifoil) were made hydrophilic by glow discharging for 60 seconds with a current of 15 mA in a PELCO easiGlow system. The cryo grids were produced using a Leica EM GP2 (Leica). The chamber was kept at 4 C and set to 95% humidity. 3 microliter sample at 0.5 mg/ml was applied to a glow-discharged holey grid, blotted for 6 s, and plunge frozen into liquid ethane and stored in liquid nitrogen..

This sample was monodisperse

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 0.7000000000000001 2.0 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20

Cryo-EM datasets were acquired with SerialEM using a Titan Krios (FEI, now ThermoFisher Scientific) operated at 300 keV and equipped with an energy filter and K3 camera (Gatan Inc.). Movies of 50 frames with a dose of 1 e-/A2 per frame (50 e-/A2 total dose) were recorded at a nominal magnification of 105,000x, corresponding to a physical pixel size of 0.83 A/px (super-resolution pixel size 0.415 A/px) in CDS mode at a dose rate of 10 e-/px/s and a defocus range of -0.7 to -2.0 um. In total, 9,656 movies were collected.

GATAN K3 BIOQUANTUM (6k x 4k) 1 3991 3.462 50.0

Cryo-EM datasets were acquired with SerialEM using a Titan Krios (FEI, now ThermoFisher Scientific) operated at 300 keV and equipped with an energy filter and K3 camera (Gatan Inc.). Movies of 50 frames with a dose of 1 e-/A2 per frame (50 e-/A2 total dose) were recorded at a nominal magnification of 105,000x, corresponding to a physical pixel size of 0.83 A/px (super-resolution pixel size 0.415 A/px) in CDS mode at a dose rate of 10 e-/px/s and a defocus range of -0.7 to -2.0 um. In total, 9,656 movies were collected.

1

Cryo-EM datasets were acquired with SerialEM using a Titan Krios (FEI, now ThermoFisher Scientific) operated at 300 keV and equipped with an energy filter and K3 camera (Gatan Inc.). Movies of 50 frames with a dose of 1 e-/A2 per frame (50 e-/A2 total dose) were recorded at a nominal magnification of 105,000x, corresponding to a physical pixel size of 0.83 A/px (super-resolution pixel size 0.415 A/px) in CDS mode at a dose rate of 10 e-/px/s and a defocus range of -0.7 to -2.0 um. In total, 9,656 movies were collected.

4802706

Good 2D class averages generated from ~1,000 manually picked particles served as templates for automatic particle picking.

4,802,706 particles were picked and extracted at 4x binned pixel size of 3.32 A and sorted by one round of 2D classification, ending up with 1,755,556 particles. Ab-initio reconstruction (K=3) was performed with the subset of particles after 2D classification. 1 C5 BACK PROJECTION 3.3 FSC 0.143 CUT-OFF cryoSPARC 3.3.2

Final non-uniform refinement by using 1,744,117 particles yielded maps at 3.3 A (with C5 symmetry applied) and 3.6 A (with C1 symmetry applied) according to gold-standard FSC = 0.143 criterion.

1744117 PROJECTION MATCHING cryoSPARC 3.3.2

SGD (stochastic gradient descent)

PROJECTION MATCHING cryoSPARC 3.3.2

Final non-uniform refinement by using 1,744,117 particles yielded maps at 3.3 A (with C5 symmetry applied) and 3.6 A (with C1 symmetry applied) according to gold-standard FSC = 0.143 criterion.

2 cryoSPARC 3.3.2

Ab-initio reconstruction (K=3) was performed with the subset of particles after 2D classification, followed byand heterogenous refinement (K=3) using all particles with C1 symmetry was applied to remove junk particles. Particles from one class (2,237,316 particles ) were re-extracted at 1x binned pixel size of 0.83 A and subjected to non-uniform refinement followed by another round of heterogenous refinement (K=2) to further sort particles.

8TUL PDB experimental model RIGID BODY FIT REAL 141.0 8TUL PDB experimental model FLEXIBLE FIT

For the MRS2-EDTA structures, models were generated from multiple rounds of manual refinement and real-space refinements with the final model of MRS2-Mg2+ as initial model.

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