9BYB | pdb_00009byb

Cryo-EM structure of the magnesium transporter MgtA in the E2 conformation with bound lipids and Mg2+

• PDB DOI: https://doi.org/10.2210/pdb9BYB/pdb
• EM Map EMD-45025: EMDB EMDataResource

• Classification: METAL TRANSPORT
• Organism(s): Lactococcus lactis subsp. lactis CV56
• Expression System: Escherichia coli O103:H2 str. 12009
• Mutation(s): Yes 


• Deposited: 2024-05-23 Released: 2025-11-26 
• Deposition Author(s): Khan, M.B., Primeau, J.O., Young, H.S.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of a membrane transport protein

Khan, M.B., Primeau, J.O., Young, H.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 201.68 kDa 
• Atom Count: 13,664 
• Modeled Residue Count: 1,764 
• Deposited Residue Count: 1,806 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnesium-transporting ATPase, P-type 1	A, B	903	Lactococcus lactis subsp. lactis CV56	Mutation(s): 8  Gene Names: LL275_1350 EC: 7.2.2.14
UniProt
Find proteins for A0A1V0NGB6 (Lactococcus lactis subsp. lactis) Explore A0A1V0NGB6  Go to UniProtKB:  A0A1V0NGB6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL (Subject of Investigation/LOI)	D [auth A], F [auth B]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
MG (Subject of Investigation/LOI)	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Khan, M.B., Primeau, J.O., Young, H.S.

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

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release
  
• Version 1.1: 2025-12-31
  Changes: Data collection, Structure summary