9GOE | pdb_00009goe

Cryo-EM structure of the multiple peptide resistance factor (MprF) from Pseudomonas aeruginosa bound to a synthetic nanobody (Sb29)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

MprF from Pseudomonas aeruginosa is a promiscuous lipid scramblase with broad substrate specificity.

Hankins, M.T.K.Parrag, M.Garaeva, A.A.Earp, J.C.Seeger, M.A.Stansfeld, P.J.Bublitz, M.

(2025) Sci Adv 11: eads9135-eads9135

  • DOI: https://doi.org/10.1126/sciadv.ads9135
  • Primary Citation of Related Structures:  
    9GOE

  • PubMed Abstract: 

    The multiple peptide resistance factor (MprF) is a bifunctional membrane protein found in many bacteria, including Pseudomonas aeruginosa and Staphylococcus aureus . MprF modifies inner leaflet lipid headgroups through aminoacylation and translocates modified lipid to the outer leaflet. This activity provides increased resistance to antimicrobial agents. MprF presents a promising target in multiresistant pathogens, but structural information is limited and both substrate specificity and energization of MprF-mediated lipid transport are poorly understood. Here, we present the cryo-EM structure of MprF from P. aeruginosa ( Pa MprF) bound to a synthetic nanobody. Pa MprF adopts an "open" conformation with a wide, lipid-exposed groove on the periplasmic side that induces a local membrane deformation in molecular dynamics simulations. Using an in vitro liposome transport assay, we demonstrate that Pa MprF translocates a wide range of different lipids without an external energy source. This suggests that Pa MprF is the first dedicated lipid scramblase to be characterized in bacteria.


  • Organizational Affiliation
    • Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylglycerol lysyltransferase885Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA0920
EC: 2.3.2.3
Membrane Entity: Yes 
UniProt
Find proteins for Q9I537 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I537 
Go to UniProtKB:  Q9I537
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I537
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Synthetic nanobody (Sybody) 29150synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom102161/Z/13/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-04-23
    Changes: Data collection, Database references