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 9R29 | pdb_00009r29

Cryo-EM structure of Acinetobacter baylyi LolDF bound AMP-PNP (closed NBDs)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9R29

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

Literature

Mechanistic basis of LolDF-mediated lipoprotein transport in Acinetobacter.

Pang, J., Chen, Y., Qiao, W., Ju, Z., Zhu, X., Chang, S., Wang, L., Zhang, Z., Zerang, Z., Xu, S., Chen, Y., Li, C., Ying, B., Ding, B.S., Chen, H., Zhang, S., Wei, X., Tang, X., Dong, H.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-76802-y
  • Primary Citation Related Structures: 
    28MF, 29EB, 9R29

  • PubMed Abstract: 

    Lipoprotein trafficking is essential for Gram-negative bacteria to maintain the outer membrane, a permeability barrier critical for survival and antibiotic resistance. While most bacteria employ the canonical LolCDE transporter, Acinetobacter utilizes a noncanonical LolDF system whose mechanism has remained unclear. Here we determine cryo-EM structures of Acinetobacter baylyi LolDF in substrate-bound, AMP-PNP-bound, and LolA-bound states. LolDF forms a symmetric homodimer with a central cavity that accommodates three acyl chains at the membrane level, suggesting lateral extraction of lipoproteins directly from the inner membrane. AMP-PNP-driven conformational changes induce a coordinated symmetric constriction of the cavity that promotes substrate expulsion, distinct from the asymmetric mechanism observed in LolCDE. Functional studies further identify key door-bar residues required for transport and reveal that charged residues at the +3 position function as an inner membrane retention signal. Together, these findings reveal a mechanistically distinct lipoprotein trafficking system and provide a framework for targeting multidrug-resistant Gram-negative pathogens.


  • Organizational Affiliation: 
    • Department of Laboratory Medicine, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.

Macromolecule Content 

  • Total Structure Weight: 139.78 kDa 
  • Atom Count: 9,822 
  • Modeled Residue Count: 1,268 
  • Deposited Residue Count: 1,268 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipoprotein-releasing system ATP-binding protein LolDA [auth B],
B [auth A]
224Acinetobacter baylyi ADP1Mutation(s): 0 
EC: 7.6.2
UniProt
Find proteins for Q9EYM2 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1))
Explore Q9EYM2 
Go to UniProtKB:  Q9EYM2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EYM2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative integral membrane proteinC [auth D],
D [auth C]
410Acinetobacter baylyi ADP1Mutation(s): 0 
UniProt
Find proteins for Q9EYM3 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1))
Explore Q9EYM3 
Go to UniProtKB:  Q9EYM3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EYM3
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31900039
National Natural Science Foundation of China (NSFC)China32170029
National Natural Science Foundation of China (NSFC)China81971974
National Natural Science Foundation of China (NSFC)China82372297

Revision History  (Full details and data files)

  • Version 1.0: 2026-11-04
    Type: Initial release