7OMM | pdb_00007omm

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

• PDB DOI: https://doi.org/10.2210/pdb7OMM/pdb
• EM Map EMD-12990: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Neisseria gonorrhoeae, synthetic construct, Methanosarcina mazei
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2021-05-24 Released: 2022-05-04 
• Deposition Author(s): 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.
• Funding Organization(s): Innosuisse

---

Experimental Data Snapshot

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

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

• PubMed: 35383177 
• DOI: https://doi.org/10.1038/s41467-022-29459-2
• Primary Citation 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.
C-CINA, Biozentrum, University of Basel, Mattenstr. 24, 4058, Basel, Switzerland.
VIB-VUB Center for Structural Biology, VIB, 1050, Brussels, Belgium.
Institute of Medical Microbiology, University of Zürich, Gloriastasse 28/30, 8006, Zürich, Switzerland.
Linkster Therapeutics AG, 8006, Zürich, Switzerland.
Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute (PSI), 5232, Villigen, Switzerland.
VIB-VUB Center for Structural Biology, VIB, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, 1050, Brussels, Belgium.
leadXpro AG, Park Innovaare, 5234, Villigen, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 219.73 kDa 
• Atom Count: 13,981 
• Modeled Residue Count: 1,794 
• Deposited Residue Count: 2,012 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly protein LptD	A	801	Neisseria gonorrhoeae	Mutation(s): 0  Gene Names: lptD, imp, ostA, NGO1715 Membrane Entity: Yes
UniProt
Find proteins for Q5F651 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F651  Go to UniProtKB:  Q5F651

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LPS-assembly lipoprotein LptE	B	165	Neisseria gonorrhoeae	Mutation(s): 0  Gene Names: lptE, F0T10_01625, F0T11_01625, F0T12_01620, WHOF_00235, WHOF_00301 Membrane Entity: Yes
UniProt
Find proteins for Q5F9V6 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5F9V6  Go to UniProtKB:  Q5F9V6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ProMacrobody 21,Maltodextrin-binding protein	C	520	synthetic construct, Methanosarcina 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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ProMacrobody 51,Maltodextrin-binding protein	D	526	synthetic construct, Methanosarcina 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

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): 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.

---

Funding Organization	Location	Grant Number
Innosuisse	Switzerland	25864.1 PFLS-LS

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2022-05-11
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Structure summary