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- PDB-9yyd: the structure of ERMA Mg2+ bound form -

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Basic information

Entry
Database: PDB / ID: 9yyd
Titlethe structure of ERMA Mg2+ bound form
ComponentsIsoform 3 of Transmembrane protein 94
KeywordsMEMBRANE PROTEIN / P-type ATPase like 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 / Chem-PEV / Transmembrane protein 94
Function and homology information
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsShi, N. / Jiang, Y.
Funding support United States, 2items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of Transmembrane protein 94
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,3163
Polymers153,5721
Non-polymers7442
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Isoform 3 of Transmembrane protein 94 / Endoplasmic reticulum magnesium ATPase


Mass: 153571.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM94, ERMA, KIAA0195 / Production host: Homo sapiens (human) / References: UniProt: Q12767
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 720.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: POPE, phospholipid*YM
Has ligand of interestY
Has protein modificationY

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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: ERMA monomer Mg++ bound form / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 967948 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028718
ELECTRON MICROSCOPYf_angle_d0.44411841
ELECTRON MICROSCOPYf_dihedral_angle_d11.3893195
ELECTRON MICROSCOPYf_chiral_restr0.0361373
ELECTRON MICROSCOPYf_plane_restr0.0041484

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