7OMT | pdb_00007omt

Crystal structure of ProMacrobody 21 with bound maltose

• PDB DOI: https://doi.org/10.2210/pdb7OMT/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Models: experimental

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.

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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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.65 kDa 
• Atom Count: 3,967 
• Modeled Residue Count: 483 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ProMacrobody 21	A	520	synthetic construct	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	C [auth A], D [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.897	α = 90
b = 87.624	β = 99.076
c = 118.635	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
PHASER	phasing

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.

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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: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary