2025-10-01 REL RCSB INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _em_admin.last_update RCSB RCSB 2023-11-13 2024-11-27 2024-11-27 2025-10-01 National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) ZIA HD008998 United States National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) ZIA HD008855 United States National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) ZIA HD008955 United States National Institutes of Health/National Library of Medicine (NIH/NLM) LM594244 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 1FI2GM146628-01 United States German Research Foundation (DFG) 3542/1-1 Germany Magnesium transporter MgtA dimer from E. coli in 5 mM MgCl2 Zeinert R Zhou F Cavalcanti Franco PH Zoeller J Lessen H Iyer A Langer JD Sodt AJ Storz G Matthies D magnesium, transport, membrane protein, dimer, oligomer, cryo-EM, P-type ATPase, ion translocation Zeinert R Zhou F Franco P Zoller J Madni ZK Lessen H Aravind L Langer JD Sodt AJ Storz G Matthies D P-type ATPase magnesium transporter MgtA acts as a dimer. Nat.Struct.Mol.Biol. US 32 1633 1643 2025 40550995 doi:10.1038/s41594-025-01593-7 1545-9985 EMD-42795 other EM volume
MgtA, Dimer, C1
 EMD-42796 other EM volume
MgtA, Monomer
 EMD-42797 other EM volume
MgtA, Dimer, ATP bound
 EMD-42798 other EM volume
MgtA, Dimer, Nonhydrolyzable ATP bound
 EMD-42799 other EM volume
MgtA, Dimer, ADP Bound
 8uy7 FULLOVERLAP EMDB EMD-42795 other EM volume
MgtA, Dimer, C1
 EMDB EMD-42796 other EM volume
MgtA, Monomer
 EMDB EMD-42797 other EM volume
MgtA, Dimer, ATP bound
 EMDB EMD-42798 other EM volume
MgtA, Dimer, Nonhydrolyzable ATP bound
 EMDB EMD-42799 other EM volume
MgtA, Dimer, ADP Bound
 EMDB EMD-42794 associated EM volume
Magnesium transporter MgtA dimer from E. coli in 5 mM MgCl2
 Magnesium transporter MgtA from Escherichia coli in the dimeric form in the presence of 5 mM MgCl2 Magnesium transporter MgtA from Escherichia coli in the dimeric form in the presence of 5 mM MgCl2 0 1 Escherichia coli Escherichia coli K-12 0.201 Magnesium-transporting ATPase, P-type 1 Escherichia coli Escherichia coli K-12 0.100393062 2 Escherichia coli LEVO MFKEIFTRLIRHLPSRLVHRDPLPGAQQTVNTVVPPSLSAHCLKMAVMPEEELWKTFDTHPEGLNQAEVESAREQHGENK LPAQQPSPWWVHLWVCYRNPFNILLTILGAISYATEDLFAAGVIALMVAISTLLNFIQEARSTKAADALKAMVSNTATVL RVINDKGENGWLEIPIDQLVPGDIIKLAAGDMIPADLRILQARDLFVAQASLTGESLPVEKAATTRQPEHSNPLECDTLC FMGTTVVSGTAQAMVIATGANTWFGQLAGRVSEQESEPNAFQQGISRVSMLLIRFMLVMAPVVLLINGYTKGDWWEAALF ALSVAVGLTPEMLPMIVTSTLARGAVKLSKQKVIVKHLDAIQNFGAMDILCTDKTGTLTQDKIVLENHTDISGKTSERVL HSAWLNSHYQTGLKNLLDTAVLEGTDEESARSLASRWQKIDEIPFDFERRRMSVVVAENTEHHQLVCKGALQEILNVCSQ VRHNGEIVPLDDIMLRKIKRVTDTLNRQGLRVVAVATKYLPAREGDYQRADESDLILEGYIAFLDPPKETTAPALKALKA SGITVKILTGDSELVAAKVCHEVGLDAGEVVIGSDIETLSDDELANLAQRTTLFARLTPMHKERIVTLLKREGHVVGFMG DGINDAPALRAADIGISVDGAVDIAREAADIILLEKSLMVLEEGVIEGRRTFANMLKYIKMTASSNFGNVFSVLVASAFL PFLPMLPLHLLIQNLLYDVSQVAIPFDNVDDEQIQKPQRWNPADLGRFMIFFGPISSIFDILTFCLMWWVFHANTPETQT LFQSGWFVVGLLSQTLIVHMIRTRRVPFIQSCASWPLMIMTVIVMIVGIALPFSPLASYLQLQALPLSYFPWLVAILAGY MTLTQLVKGFYSRRYGWQHHHHHH P0ABB8 MAGNESIUM ION 2.4305e-05 6 MG water 1.8015e-05 200 HOH singleParticle particle 3.2 7.5
50 mM Tris/HCl pH 7.5, 50 mM K2SO4, 5 mM MgCl2, 0.007% glycol-diosgenin, 2 mM DTT
 Quantifoil R1.2/1.3 COPPER 400 GLOW DISCHARGE
Quantifoil R1.2/1.3 400 copper mesh grids (EMS) were glow discharged in a PELCO easiGlow Glow Discharge Cleaning System (Ted Pella) at 15 mA for 1 min.
 ETHANE 88 278 LEICA EM GP
Quantifoil R1.2/1.3 400 copper mesh grids (EMS) were glow discharged in a PELCO easiGlow Glow Discharge Cleaning System (Ted Pella) at 15 mA for 1 min. A 3 microliter sample at a concentration of 3.2 mg/mL was applied to the glow discharged grids. After blotting for 5 s in a Leica GP-EM2 plunger (Leica Microsystems, Wetzlar, Germany) with the chamber set to 5 degrees C and 95% humidity, the grids were immediately plunge frozen into liquid ethane and stored in liquid nitrogen..
E. coli MgtA purified with a C-terminal His-tag
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.0 2.0 105000.0 60241.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 2 17152 4.31 60.0
A first dataset was collected with a dose rate of 9.5 A/px/s (~7.5 on the camera through the sample), exposure time 0.0712 s/frame (~1 e-/A2) and total exposure time of 4.31 s per movie (~60 e-/A2), resulting in a total of 10,246 movies with 60 frames each. A second dataset was collected with a dose rate of 10 A/px/s (~7.5 on the camera through the sample), exposure time 0.0668 s/frame (~1 e-/A2) and total exposure time of 3.46 s per movie (~50 e-/A2), resulting in a total of 6906 movies with 50 frames each.
 1 3353940
1,578,214 particles were initially selected from dataset 1 (10,164 selected movies from 10,246 total). 1,775,726 particles were initially selected from dataset 2 (5,778 selected movies from 6,906 total).
 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION C2 BACK PROJECTION 2.93 FSC 0.143 CUT-OFF cryoSPARC 160139 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC cryoSPARC emd_42794.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -3.4739537 5.6103983 0.009281112 0.113711864 0.83 0.83 0.83 1.05 AUTHOR Single-particle cryo-EM map of magnesium transporter MgtA from Escherichia coli in the dimeric form in the presence of 5 mM MgCl2 at an overall resolution of 2.93 A, filtered to local resolution AlphaFold in silico model RIGID BODY FIT REAL AlphaFold in silico model FLEXIBLE FIT REAL AlphaFold in silico model FLEXIBLE FIT REAL emd_42794_msk_1.map emd_42794_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -7.859277 11.62487 0.0044628517 0.2209633 0.83 0.83 0.83 AUTHOR Sharpened map after refinement emd_42794_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -1.2066283 2.8283837 0.0044628517 0.07882681 0.83 0.83 0.83 AUTHOR Non sharpened map after refinement emd_42794_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -1.4747941 3.2556412 0.005073069 0.14458968 0.83 0.83 0.83 AUTHOR Half map A emd_42794_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 318.72 318.72 318.72 90.0 90.0 90.0 X Y Z -1.5841359 3.109551 0.0050938795 0.14425337 0.83 0.83 0.83 AUTHOR Half map B