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- EMDB-73556: the structure of ERMA complex with ATPrS and Mg++ -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-73556
Titlethe structure of ERMA complex with ATPrS and Mg++
Map datastructure of ERMA complex with ATPrS and Mg
Sample
  • Complex: ERMA
    • Protein or peptide: Transmembrane protein 94
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: N-OCTANE
KeywordsP-type ATPase like protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


magnesium ion transport from cytosol to endoplasmic reticulum / intracellular magnesium ion homeostasis / P-type magnesium transporter activity / embryonic heart tube development / embryonic brain development / endoplasmic reticulum membrane / nucleoplasm
Similarity search - Function
Transmembrane protein 94 / P-type ATPase, transmembrane domain superfamily
Similarity search - Domain/homology
Transmembrane protein 94
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 24, 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_73556.png

Downloads & links

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Map

FileDownload / File: emd_73556.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of ERMA complex with ATPrS and Mg
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.04 Å/pix.
x 240 pix.
= 249.408 Å		1.04 Å/pix.
x 240 pix.
= 249.408 Å		1.04 Å/pix.
x 240 pix.
= 249.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0392 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.7
Minimum - Maximum-30.080321999999999 - 44.021144999999997
Average (Standard dev.)-0.000000000001313 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.40799 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_73556_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_73556_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

EntireName: ERMA
Components
  • Complex: ERMA
    • Protein or peptide: Transmembrane protein 94
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: N-OCTANE

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Supramolecule #1: ERMA

SupramoleculeName: ERMA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 154 kDa/nm

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Macromolecule #1: Transmembrane protein 94

MacromoleculeName: Transmembrane protein 94 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 156.281734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG GSLETMDLRE KHLGEPPLAL GLSTRKALSV LKEQLEAVLE KHLKERKKSL TWKEAWRSSF LHLSNRCSCF HWPGASLML LAVLLLLCCC GGQPAGSQGV ELVNASALFL LLLLNLVLIG RQDRLKRREV ERRLRGIIDQ IQDALRDGKE I KWPNSMYP ...String:
MDYKDDDDKG GSLETMDLRE KHLGEPPLAL GLSTRKALSV LKEQLEAVLE KHLKERKKSL TWKEAWRSSF LHLSNRCSCF HWPGASLML LAVLLLLCCC GGQPAGSQGV ELVNASALFL LLLLNLVLIG RQDRLKRREV ERRLRGIIDQ IQDALRDGKE I KWPNSMYP DLHMPFAPSW SLHWAYRDGH LVNLPVSLLV EGDIIALRPG QESFASLRGI KDDEHIVLEP GDLFPPFSPP PS PRGEVKR GPQNPQQHRL FRVLETPVID NIRWCLDTAL SRPVTALDNE RFTVQSVMLH YAVPVVLAGF LITNALRFMF KAP GVTSWQ YTLLQLQVNG MLPILPLLFP VLWVLATACG EARVLAQMSK ASPSSLLAKF SEDTLSSYTE AVSSQEMLRC IWGH FLRVI QGTSPTLSHS ASLLHSLGSV TVLCCVDKQG ILSWPNPSPE TVLFFSGKVE PPHSSHEDLT DDLSTRSFCH PEVEE EPHE HDALLAGSLN NTLHLSNEQE RSDWLADGPK PSEPYPHHKG HGRSKHPSGS NVSFSRDTEG GEEEPSKAQP GTEGDP YEA EDFVCDYHLE MLSLSQDQQN PSCIQFDDSN WQSHLTSLKP LGLNVLLNLC NASVTERLCR FSDHLCNIAL QESHSAV LP VHVPWGLCEL ARLIGFTPGA KELFKQENHL ALYRLPSAET LKETSLGRPS CVTKRRPPLS HMISLFIKDT ATSTEQML S HGSADVVVEA CTDFWDGADI YPLSGSDRKK VLDFYQRACL SGYCSAFAYK PMNCTLSSQL NGKCIELVQV PGQNSIFTM CELPSTIPIK PNNRRSSWSS DEGIGEVLEK EDCMQALSGQ IFMGMVSSQY QARLDIVRLI DGLVNACIRF VYFSLEDELR SKVFAEKMG LETGWNCHIS LTPNGDMPGS EIPPSSPSHA GSLHDDLNQV SRDDAEGLLL LEEEGHSDLI SFQPTDSDIP S FLEDCNRA KLPRGIHQVR PHLQNIDNVP LLVPLFTDCT PDTMCEMIKI MQEYGEVTCC LGSSANLRNS CLFLQSDVSI AL DPLYPSR CSWETFGYAT STTMAQASDG LSPLQLSGQL NSLPCSLTFR QEESISIIRL IEQARHATYG IRKCFLFLLQ CQL TLVVIQ FLSCLVQLPP LLSTTDILWL SCFCYPLLSI SLLGKPPHSS IMSMATGKNL QSIPKKTQHY FLLCFLLKFS LTIS SCLVC FGFTLQSFCD SARARNLTNC SSVMLCSNDD RAPAWFEDFA NGLLSAQKLT AALIVLHTVF ISITHVHRTK PLWRK SPLT NLWWAVTVPV VLLGQVVQTV VDLQLWTHRD SRVHFGLEDV PLLTWLLGCL SLVLVVVTNE IVKLHEIRVR VRYQKR QKL QFETKLGMNS PFAAATAGIR GTKLNQPLDY KIFSVTE

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: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 1 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #4: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 4 / Number of copies: 9 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #5: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 5 / Number of copies: 3 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #6: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 6 / Number of copies: 1 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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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
Sample stageCooling holder cryogen: NITROGEN
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 272680
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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