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- EMDB-73879: Human NIPA2 mutant A75T -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-73879
TitleHuman NIPA2 mutant A75T
Map datamain map
Sample
  • Organelle or cellular component: Human NIPA2 A75T mutant
    • Protein or peptide: Magnesium transporter NIPA2
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordsmembrane protein / transporter / TRANSPORT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKaruppan SJ / Connolly N / Shrestha S / Medearis M / Gholampour M / Zubcevic L
Funding support1 items
OrganizationGrant numberCountry
Other privateKlingenstein-Simons Neuroscience Fellowship
CitationJournal: Nat Commun / Year: 2026
Title: Mechanistic studies of the human NIPA2 transporter
Authors: Karuppan SJ / Connolly N / Shrestha S / Medearis M / Gholampour M / Zubcevic L
History
DepositionNov 17, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73879.png

Downloads & links

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Map

FileDownload / File: emd_73879.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.1846932 - 1.5770491
Average (Standard dev.)-0.000040463266 (±0.027951218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.104 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_73879_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_73879_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human NIPA2 A75T mutant

EntireName: Human NIPA2 A75T mutant
Components
  • Organelle or cellular component: Human NIPA2 A75T mutant
    • Protein or peptide: Magnesium transporter NIPA2
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Human NIPA2 A75T mutant

SupramoleculeName: Human NIPA2 A75T mutant / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.97 KDa

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Macromolecule #1: Magnesium transporter NIPA2

MacromoleculeName: Magnesium transporter NIPA2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.013812 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSQGRGKYDF YIGLGLAMSS SIFIGGSFIL KKKGLLRLAR KGSMRAGQGG HAYLKEWLWW AGLLSMGAGE VANFTAYAFA PATLVTPLG ALSVLVSAIL SSYFLNERLN LHGKIGCLLS ILGSTVMVIH APKEEEIETL NEMSHKLGDP GFVVFATLVV I VALILIFV ...String:
MSQGRGKYDF YIGLGLAMSS SIFIGGSFIL KKKGLLRLAR KGSMRAGQGG HAYLKEWLWW AGLLSMGAGE VANFTAYAFA PATLVTPLG ALSVLVSAIL SSYFLNERLN LHGKIGCLLS ILGSTVMVIH APKEEEIETL NEMSHKLGDP GFVVFATLVV I VALILIFV VGPRHGQTNI LVYITICSVI GAFSVSCVKG LGIAIKELFA GKPVLRHPLA WILLLSLIVC VSTQINYLNR AL DIFNTSI VTPIYYVFFT TSVLTCSAIL FKEWQDMPVD DVIGTLSGFF TIIVGIFLLH AFKDVSFSLA SLPVSFRKDE KAM NGNLSN MYEVLNNNEE SLTCGIEQHT GENVSRRNGN LTAFSNSLEV LFQGPAADYK DDDDKAHHHH HHHHHH

UniProtKB: Magnesium transporter NIPA2

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Macromolecule #2: MAGNESIUM ION

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

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1.6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
50.0 mMC4H11NO3Tris
2.0 mMMgCl2Magnesium Chloride
2.0 mMC4H10O2S2Dithiothreitol
0.1 mMC47H88O22Lauryl Maltose Neopentyl Glycol
0.02 mMC35H61NO7Cholesteryl Hemisuccinate Tris Salt
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.042 kPa / Details: 3x (45s, 0.42 mBar, 15 mAmps)
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 19064 / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 13300000
CTF correctionSoftware - Name: cryoSPARC (ver. 4+) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4+) / Number images used: 284521
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4+)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4+)
Final 3D classificationNumber classes: 6 / Software - Name: cryoSPARC (ver. 4+) / Software - details: Ab initio

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Atomic model buiding 1

Initial modelPDB ID:

9z6n


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9z7s:
Human NIPA2 mutant A75T

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