9N5J | pdb_00009n5j

Cryo-EM structure of the magnesium transporter MgtA in the E2 conformation with bound beryllium fluoride (BeF3-) and Mg2+ at 2.65 A resolution.

PDB DOI: https://doi.org/10.2210/pdb9N5J/pdb
EM Map EMD-48923: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Lactococcus lactis subsp. lactis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-02-04 Released: 2026-02-18
Deposition Author(s): Khan, M.B., Primeau, J.O., Basu, P.C., Morth, J.P., Lemieux, M.J., Young, H.S.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.59 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9N5J

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of a membrane transport protein

Khan, M.B., Primeau, J.O., Basu, P.C., Morth, J.P., Lemieux, M.J., Young, H.S.

To be published.

Macromolecule Content

Total Structure Weight: 203.24 kDa
Atom Count: 13,686
Modeled Residue Count: 1,778
Deposited Residue Count: 1,842
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnesium-transporting ATPase, P-type 1	A, B [auth C]	921	Lactococcus lactis subsp. lactis	Mutation(s): 0 Gene Names: LL275_1350 EC: 7.2.2.14
UniProt
Find proteins for A0A1V0NGB6 (Lactococcus lactis subsp. lactis) Explore A0A1V0NGB6 Go to UniProtKB: A0A1V0NGB6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1V0NGB6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BEF (Subject of Investigation/LOI) Query on BEF Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain E [auth A]	E [auth A], H [auth C]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain F [auth C] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth C] MOL2 format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth C] mmCIF format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth C], G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth C] Focus chain G [auth C] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth C] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.59 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2026-02-18
Type: Initial release
Version 1.1: 2026-03-04
Changes: Data collection, Structure summary

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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.