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- EMDB-73630: the structure of ERMA Mg2+ bound form -

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Basic information

Entry
Database: EMDB / ID: EMD-73630
Titlethe structure of ERMA Mg2+ bound form
Map datastructure of ERMA Mg2+ bound form
Sample
  • Complex: ERMA monomer Mg++ bound form
    • Protein or peptide: Isoform 3 of Transmembrane protein 94
  • Ligand: MAGNESIUM ION
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
KeywordsP-type ATPase like protein / MEMBRANE PROTEIN
Function / homologymagnesium ion transport from cytosol to endoplasmic reticulum / Transmembrane protein 94 / intracellular magnesium ion homeostasis / P-type magnesium transporter activity / P-type ATPase, transmembrane domain superfamily / endoplasmic reticulum membrane / nucleoplasm / Transmembrane protein 94
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsShi N / Jiang Y
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140892 United States
CitationJournal: Sci Adv / Year: 2026
Title: Structural and mutational insights define ERMA as the ER Mg ATPase and reservoir gatekeeper.
Authors: Manigandan Venkatesan / Michael L Oldham / Ning Shi / Adhishree Chidambaram / Neelanjan Vishnu / Abitha K Madesh / Kristen Bentz / Peter B Stathopulos / Ravi C Kalathur / Youxing Jiang / Muniswamy Madesh /
Abstract: Magnesium (Mg) is the most abundant divalent cation in cells, yet the mechanisms mediating its organellar transport remain poorly defined. We identify endoplasmic reticulum (ER) Mg adenosine ...Magnesium (Mg) is the most abundant divalent cation in cells, yet the mechanisms mediating its organellar transport remain poorly defined. We identify endoplasmic reticulum (ER) Mg adenosine triphosphatase (ATPase) (ERMA) as the transporter that drives Mg uptake into the ER lumen, establishing the ER as a bi-ionic intracellular reservoir. MagFRET biosensors targeted to the ER demonstrate that ERMA mediates dynamic ER Mg storage and robust adenosine 5'-triphosphate-dependent Mg uptake reaching 15 to 30 millimolar. Cryo-electron microscopy structures of human and mouse ERMA reveal a P-type ATPase fold with an unwound transmembrane 4 (TM4) that coordinates Mg via the unique PILP backbone and the TM5 residue Q1110, whose mutation markedly impairs ERMA-mediated Mg uptake. Functional reconstitution of domain mutants, ERMA-SERCA chimeras, and pathogenic variants confirm ERMA as an ER-resident Mg pump and gatekeeper of ER Mg ionic equilibrium.
History
DepositionOct 28, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73630.png

Downloads & links

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Map

FileDownload / File: emd_73630.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of ERMA Mg2+ bound form
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.83 Å/pix.
x 288 pix.
= 238.176 Å		0.83 Å/pix.
x 288 pix.
= 238.176 Å		0.83 Å/pix.
x 288 pix.
= 238.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.9
Minimum - Maximum-17.205300999999999 - 35.973930000000003
Average (Standard dev.)-0.000000000001511 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 238.17601 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_73630_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_73630_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ERMA monomer Mg++ bound form

EntireName: ERMA monomer Mg++ bound form
Components
  • Complex: ERMA monomer Mg++ bound form
    • Protein or peptide: Isoform 3 of Transmembrane protein 94
  • Ligand: MAGNESIUM ION
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

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Supramolecule #1: ERMA monomer Mg++ bound form

SupramoleculeName: ERMA monomer Mg++ bound form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 3 of Transmembrane protein 94

MacromoleculeName: Isoform 3 of Transmembrane protein 94 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 153.571797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKM LFKQAELWMP HQGKGNKGEP PSALGLSTRK ALSVLKEQLE AVLEGHLRER KKCLTWKEVW RSSFLHHSNR CSCFHWPGA SLMLLAVLLL LGCCGGQPAG SRGVGLVNAS ALFLLLLLNL VLIGRQDRLK RREVERRLRG IIDQIQDALR D GREIQWPS ...String:
MDYKDDDDKM LFKQAELWMP HQGKGNKGEP PSALGLSTRK ALSVLKEQLE AVLEGHLRER KKCLTWKEVW RSSFLHHSNR CSCFHWPGA SLMLLAVLLL LGCCGGQPAG SRGVGLVNAS ALFLLLLLNL VLIGRQDRLK RREVERRLRG IIDQIQDALR D GREIQWPS AMYPDLHMPF APSWSLHWAY RDGHLVNLPV SLLVEGDIIA LRPGQESFAS LRGIKDDEHI VLEPGDLFPP FS PPPSPRG EVERGPQSPQ QHRLFRVLET PVIDNIRWCL DMALSRPVTA LDNERFTVQS VMLHYAVPVV LAGFLITNAL RFI FSAPGV TSWQYTLLQL QVNGVLPILP LLFPVLWVLA TACGEARVLA QMSKASPSSL LAKFSEDTLS SYTEAVSSQE MLRC IWGHF LRVLGGTSPT LSHSSSLLHS LGSVTVLCCV DKQGILSWPN PSPETVLFFS GKVEPPHSSH EDLTDGLSTR SFCHP EPHE RDALLAGSLN NTLHLSNEQE RGDWPGEAPK PPEPYSHHKA HGRSKHPSGS NVSFSRDTEG GEEEPSKTQP GMESDP YEA EDFVCDYHLE MLSLSQDQQN PSCIQFDDSN WQLHLTSLKP LGLNVLLNLC DASVTERLCR FSDHLCNIAL QESHSAV LP VHVPWGLCEL ARLIGFTPGA KELFKQENHL ALYRLPSAET MKETSLGRLS CVTKRRPPLS HMISLFIKDT TTSTEQML S HGTADVVLEA CTDFWDGADI YPLSGSDRKK VLDFYQRACL SGYCSAFAYK PMNCALSSQL NGKCIELVQV PGQSSIFTM CELPSTIPIK QNARRSSWSS DEGIGEVLEK EDCMQALSGQ IFMGMVSSQY QARLDIVRLI DGLVNACIRF VYFSLEDELK SKVFAEKMG LETGWNCHIS LTPNGDMPGS EIPPSSPSHA GSLHDDLNQV SRDDAEGLLL MEEEGHSDLI SFQPTDSDIP S FLEDSNRA KLPRGIHQVR PHLQNIDNVP LLVPLFTDCT PETMCEMIKI MQEYGEVTCC LGSSANLRNS CLFLQSDISI AL DPLYPSR CSWETFGYAT SISMAQASDG LSPLQLSGQL NSLPCSLTFR QEETISIIRL IEQARHATYG IRKCFLFLLQ CQL TLVVIQ FLSCLVQLPP LLSTTDILWL SCFCYPLLSI SLLGKPPHSS IMSMATGKNL QSIPKKTQHY FLLCFLLKFS LTLS SCLIC FGFTLQSFCD SSRDRNLTNC SSVMLPSNDD RAPAWFEDFA NGLLSAQKLT AALIVLHTVF ISITHVHRTK PLWRK SPLT NLWWAVTVPV VLLGQVVQTA VDLQLWTHRD SHVHFGLEDV PLLTWLLGCL SLVLVVVTNE IVKLHEIRVR VRYQKR QKL QFETKLGMNS PF

UniProtKB: Transmembrane protein 94

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 3 / Number of copies: 1 / Formula: PEV
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 967948
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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