9Z7T | pdb_00009z7t

Human NIPA2 with ATP

PDB DOI: https://doi.org/10.2210/pdb9Z7T/pdb
EM Map EMD-73880: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-11-17 Released: 2026-07-29
Deposition Author(s): Karuppan, S.J., Connolly, N., Shrestha, S., Medearis, M., Gholampour, M., Zubcevic, L.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9Z7T

This is version 1.0 of the entry. See complete history.

Literature

Mechanistic studies of the human NIPA2 transporter

Karuppan, S.J., Connolly, N., Shrestha, S., Medearis, M., Gholampour, M., Zubcevic, L.

(2026) Nat Commun

DOI: https://doi.org/10.1038/s41467-026-75832-w

Macromolecule Content

Total Structure Weight: 86.5 kDa
Atom Count: 4,125
Modeled Residue Count: 595
Deposited Residue Count: 784
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnesium transporter NIPA2	A, B	392	Homo sapiens	Mutation(s): 0 Gene Names: NIPA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N8Q9 (Homo sapiens) Explore Q8N8Q9 Go to UniProtKB: Q8N8Q9
GTEx: ENSG00000140157
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N8Q9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4+

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		Klingenstein-Simons Neuroscience Fellowship

Revision History (Full details and data files)

Version 1.0: 2026-07-29
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.