6YFY | pdb_00006yfy

Solid-state NMR structure of the D-Arg4,L10-teixobactin - Lipid II complex in lipid bilayers.


Experimental Data Snapshot

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 26 
  • Conformers Submitted: 26 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report

Validation slider image for 6YFY

This is version 5.0 of the entry. See complete history

Literature

Mode of action of teixobactins in cellular membranes.

Shukla, R.Medeiros-Silva, J.Parmar, A.Vermeulen, B.J.A.Das, S.Paioni, A.L.Jekhmane, S.Lorent, J.Bonvin, A.M.J.J.Baldus, M.Lelli, M.Veldhuizen, E.J.A.Breukink, E.Singh, I.Weingarth, M.

(2020) Nat Commun 11: 2848-2848

  • DOI: https://doi.org/10.1038/s41467-020-16600-2
  • Primary Citation Related Structures: 
    6YFY

  • PubMed Abstract: 

    The natural antibiotic teixobactin kills pathogenic bacteria without detectable resistance. The difficult synthesis and unfavourable solubility of teixobactin require modifications, yet insufficient knowledge on its binding mode impedes the hunt for superior analogues. Thus far, teixobactins are assumed to kill bacteria by binding to cognate cell wall precursors (Lipid II and III). Here we present the binding mode of teixobactins in cellular membranes using solid-state NMR, microscopy, and affinity assays. We solve the structure of the complex formed by an improved teixobactin-analogue and Lipid II and reveal how teixobactins recognize a broad spectrum of targets. Unexpectedly, we find that teixobactins only weakly bind to Lipid II in cellular membranes, implying the direct interaction with cell wall precursors is not the sole killing mechanism. Our data suggest an additional mechanism affords the excellent activity of teixobactins, which can block the cell wall biosynthesis by capturing precursors in massive clusters on membranes.


  • Organizational Affiliation
    • NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 10.61 kDa 
  • Atom Count: 704 
  • Modeled Residue Count: 64 
  • Deposited Residue Count: 64 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
D-Arg4,Leu10-TeixobactinA,
B,
C [auth E],
D [auth F]
11Eleftheria terraeMutation(s): 0 
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipid IIE [auth C],
F [auth D],
G,
H
5Staphylococcus simulansMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid
I, J, K, L
2N/A
Glycosylation Resources
GlyTouCan: G88499BX
GlyCosmos: G88499BX

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P1W

Query on P1W



Download:Ideal Coordinates CCD File
AA [auth F]
DA [auth F]
EA [auth F]
FA [auth F]
O [auth A]
AA [auth F],
DA [auth F],
EA [auth F],
FA [auth F],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
V [auth B],
Y [auth E],
Z [auth F]
3-methylbut-2-en-1-ol
C5 H10 O
ASUAYTHWZCLXAN-UHFFFAOYSA-N
2PO

Query on 2PO



Download:Ideal Coordinates CCD File
BA [auth F]
CA [auth F]
M [auth A]
N [auth A]
T [auth B]
BA [auth F],
CA [auth F],
M [auth A],
N [auth A],
T [auth B],
U [auth B],
W [auth E],
X [auth E]
PHOSPHONATE
H O3 P
ABLZXFCXXLZCGV-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 

3 Unique

Experimental Data & Validation

Experimental Data

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 26 
  • Conformers Submitted: 26 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands723.014.003
Netherlands Organisation for Scientific Research (NWO)Netherlands711.018.001
Netherlands Organisation for Scientific Research (NWO)Netherlands700.26.121
Netherlands Organisation for Scientific Research (NWO)Netherlands700.10.443

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2020-08-19
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.1: 2021-09-15
    Changes: Advisory, Database references, Derived calculations
  • Version 3.2: 2023-05-17
    Changes: Structure summary
  • Version 4.0: 2023-11-15
    Changes: Atomic model, Data collection
  • Version 5.0: 2024-08-07
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations