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- PDB-9z6n: Human NIPA2 transporter in the presence of EDTA -

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Basic information

Entry
Database: PDB / ID: 9z6n
TitleHuman NIPA2 transporter in the presence of EDTA
ComponentsMagnesium transporter NIPA2
KeywordsTRANSPORT PROTEIN / membrane protein / transporter
Function / homology
Function and homology information


magnesium ion transport / Miscellaneous transport and binding events / magnesium ion transmembrane transporter activity / early endosome / membrane / plasma membrane
Similarity search - Function
Magnesium transporter NIPA / Magnesium transporter NIPA / :
Similarity search - Domain/homology
Magnesium transporter NIPA2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKaruppan, S.J. / Connolly, N. / Shrestha, S. / Medearis, M. / Gholampour, M. / Zubcevic, L.
Funding support1items
OrganizationGrant numberCountry
Other privateKlingenstein-Simons Neuroscience Fellowship
CitationJournal: Nat Commun / Year: 2026
Title: Mechanistic studies of the human NIPA2 transporter
Authors: Karuppan, S.J. / Connolly, N. / Shrestha, S. / Medearis, M. / Gholampour, M. / Zubcevic, L.
History
DepositionNov 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Magnesium transporter NIPA2
B: Magnesium transporter NIPA2


Theoretical massNumber of molelcules
Total (without water)85,9682
Polymers85,9682
Non-polymers00
Water00
1


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

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Components

#1: Protein Magnesium transporter NIPA2 / Non-imprinted in Prader-Willi/Angelman syndrome region protein 2


Mass: 42983.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NIPA2 / Plasmid: pFB-FLAG-HIS / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8N8Q9
Has protein modificationN

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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: Human NIPA2 transporter in the presence of EDTA / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.04297 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Plasmid: pFB-FLAG-HIS
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
250 mMTrisC4H11NO31
32 mMEDTAC10H16N2O81
42 mMDithiothreitolC4H10O2S21
50.1 mMLauryl Maltose Neopentyl GlycolC47H88O221
60.02 mMCholesteryl Hemisuccinate Tris SaltC35H61NO71
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 150mM NaCL, 50mM Tris pH 8.0, 2 mM EDTA, 2 mM DTT, 0.1 mM LMNG, 0.02 mM CHS
Specimen supportDetails: 3x(15mA, 45s glow, 0.42mBar) / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 293.15 K

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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: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14453
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4+particle selectionmanual picking, template picking
2SerialEMimage acquisition
4cryoSPARC4+CTF correctionPatch CTF
7UCSF Chimeramodel fitting
8Cootmodel fitting
10cryoSPARC4+initial Euler assignment
11cryoSPARC4+final Euler assignment
12cryoSPARC4+classification2D Class
13cryoSPARC4+3D reconstruction
14PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8900000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135512 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingAccession code: Q8N8Q9 / Source name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.7 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024445
ELECTRON MICROSCOPYf_angle_d0.4036071
ELECTRON MICROSCOPYf_dihedral_angle_d12.771632
ELECTRON MICROSCOPYf_chiral_restr0.034751
ELECTRON MICROSCOPYf_plane_restr0.003743

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