8I8X

Cryo-EM Structure of OmpC3-MlaA-MlaC Complex in MSP2N2 Nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 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

Molecular mechanism of phospholipid transport at the bacterial outer membrane interface.

Yeow, J.Luo, M.Chng, S.S.

(2023) Nat Commun 14: 8285-8285

  • DOI: https://doi.org/10.1038/s41467-023-44144-8
  • Primary Citation of Related Structures:  
    8I8R, 8I8X

  • PubMed Abstract: 

    The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer with outer leaflet lipopolysaccharides and inner leaflet phospholipids (PLs). This unique lipid asymmetry renders the OM impermeable to external insults, including antibiotics and bile salts. To maintain this barrier, the OmpC-Mla system removes mislocalized PLs from the OM outer leaflet, and transports them to the inner membrane (IM); in the first step, the OmpC-MlaA complex transfers PLs to the periplasmic chaperone MlaC, but mechanistic details are lacking. Here, we biochemically and structurally characterize the MlaA-MlaC transient complex. We map the interaction surfaces between MlaA and MlaC in Escherichia coli, and show that electrostatic interactions are important for MlaC recruitment to the OM. We further demonstrate that interactions with MlaC modulate conformational states in MlaA. Finally, we solve a 2.9-Å cryo-EM structure of a disulfide-trapped OmpC-MlaA-MlaC complex in nanodiscs, reinforcing the mechanism of MlaC recruitment, and highlighting membrane thinning as a plausible strategy for directing lipids for transport. Our work offers critical insights into retrograde PL transport by the OmpC-Mla system in maintaining OM lipid asymmetry.


  • Organizational Affiliation

    Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane porin C
A, B, C
346Escherichia coli K-12Mutation(s): 0 
Gene Names: ompCmeoAparb2215JW2203
UniProt
Find proteins for P06996 (Escherichia coli (strain K12))
Explore P06996 
Go to UniProtKB:  P06996
Entity Groups  
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UniProt GroupP06996
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Intermembrane phospholipid transport system lipoprotein MlaA234Escherichia coli K-12Mutation(s): 1 
Gene Names: mlaAvacJb2346JW2343
UniProt
Find proteins for P76506 (Escherichia coli (strain K12))
Explore P76506 
Go to UniProtKB:  P76506
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UniProt GroupP76506
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Intermembrane phospholipid transport system binding protein MlaCE [auth F]199Escherichia coli K-12Mutation(s): 1 
Gene Names: mlaCyrbCb3192JW3159
UniProt
Find proteins for P0ADV7 (Escherichia coli (strain K12))
Explore P0ADV7 
Go to UniProtKB:  P0ADV7
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UniProt GroupP0ADV7
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KDL
Query on KDL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth B],
H [auth C]
(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]-5-oxidanyl-oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid
C110 H202 N2 O39 P2
DIXUKJUHGLIZGU-OIPVZEHTSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0.0
MODEL REFINEMENTCoot0.9.4.1 EL
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentSingaporeMOH-000145

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Database references