7OMM

Cryo-EM structure of N. gonorhoeae LptDE in complex with ProMacrobodies (MBPs have not been built de novo)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

Cryo-EM structures of a LptDE transporter in complex with Pro-macrobodies offer insight into lipopolysaccharide translocation.

Botte, M.Ni, D.Schenck, S.Zimmermann, I.Chami, M.Bocquet, N.Egloff, P.Bucher, D.Trabuco, M.Cheng, R.K.Y.Brunner, J.D.Seeger, M.A.Stahlberg, H.Hennig, M.

(2022) Nat Commun 13: 1826-1826

  • DOI: https://doi.org/10.1038/s41467-022-29459-2
  • Primary Citation of Related Structures:  
    7OMM, 7OMT

  • PubMed Abstract: 

    Lipopolysaccharides are major constituents of the extracellular leaflet in the bacterial outer membrane and form an effective physical barrier for environmental threats and for antibiotics in Gram-negative bacteria. The last step of LPS insertion via the Lpt pathway is mediated by the LptD/E protein complex. Detailed insights into the architecture of LptDE transporter complexes have been derived from X-ray crystallography. However, no structure of a laterally open LptD transporter, a transient state that occurs during LPS release, is available to date. Here, we report a cryo-EM structure of a partially opened LptDE transporter in complex with rigid chaperones derived from nanobodies, at 3.4 Å resolution. In addition, a subset of particles allows to model a structure of a laterally fully opened LptDE complex. Our work offers insights into the mechanism of LPS insertion, provides a structural framework for the development of antibiotics targeting LptD and describes a highly rigid chaperone scaffold to enable structural biology of challenging protein targets.


  • Organizational Affiliation

    leadXpro AG, Park Innovaare, 5234, Villigen, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LPS-assembly protein LptD801Neisseria gonorrhoeaeMutation(s): 0 
Gene Names: lptDimpostANGO1715
Membrane Entity: Yes 
UniProt
Find proteins for Q5F651 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Explore Q5F651 
Go to UniProtKB:  Q5F651
Entity Groups  
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UniProt GroupQ5F651
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LPS-assembly lipoprotein LptE165Neisseria gonorrhoeaeMutation(s): 0 
Gene Names: lptEF0T10_01625F0T11_01625F0T12_01620WHOF_00235WHOF_00301
Membrane Entity: Yes 
UniProt
Find proteins for Q5F9V6 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Explore Q5F9V6 
Go to UniProtKB:  Q5F9V6
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UniProt GroupQ5F9V6
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ProMacrobody 21,Maltodextrin-binding protein520synthetic constructMethanosarcina mazei
This entity is chimeric
Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
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UniProt GroupP0AEX9
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ProMacrobody 51,Maltodextrin-binding protein526synthetic constructMethanosarcina mazei
This entity is chimeric
Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
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UniProt GroupP0AEX9
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
InnosuisseSwitzerland25864.1 PFLS-LS

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references