[English] 日本語
Yorodumi
- EMDB-73880: Human NIPA2 with ATP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73880
TitleHuman NIPA2 with ATP
Map dataMain map
Sample
  • Organelle or cellular component: Human NIPA2 with ATP
    • Protein or peptide: Magnesium transporter NIPA2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • 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: 3.9 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

-
Structure visualization

Supplemental images

emd_73880.png

Downloads & links

-
Map

FileDownload / File: emd_73880.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.
= 270.515 Å		1.06 Å/pix.
x 256 pix.
= 270.515 Å		1.06 Å/pix.
x 256 pix.
= 270.515 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0567 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.9345811 - 1.5249481
Average (Standard dev.)-0.0003119241 (±0.03060879)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 270.5152 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map A

Fileemd_73880_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_73880_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human NIPA2 with ATP

EntireName: Human NIPA2 with ATP
Components
  • Organelle or cellular component: Human NIPA2 with ATP
    • Protein or peptide: Magnesium transporter NIPA2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

-
Supramolecule #1: Human NIPA2 with ATP

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

-
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: 42.983785 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSQGRGKYDF YIGLGLAMSS SIFIGGSFIL KKKGLLRLAR KGSMRAGQGG HAYLKEWLWW AGLLSMGAGE VANFAAYAFA PATLVTPLG ALSVLVSAIL SSYFLNERLN LHGKIGCLLS ILGSTVMVIH APKEEEIETL NEMSHKLGDP GFVVFATLVV I VALILIFV ...String:
MSQGRGKYDF YIGLGLAMSS SIFIGGSFIL KKKGLLRLAR KGSMRAGQGG HAYLKEWLWW AGLLSMGAGE VANFAAYAFA 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

-
Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
50.0 mMC4H11NO3Tris
0.5 mMC10H12Mg2N5O13P3Adenosine 5 triphosphate magnesium salt
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, 42 mBar, 15 mAmps)
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP

-
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: 11882 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3300000
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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4+) / Number images used: 157559
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4+)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4+)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4+) / Software - details: Ab initio

-
Atomic model buiding 1

Initial modelPDB ID:

9z6n


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

PDB-9z7t:
Human NIPA2 with ATP

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more