7PDC

The structure of the human tetrameric LL-37 peptide in a channel conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of the antimicrobial human cathelicidin LL-37 shows oligomerization and channel formation in the presence of membrane mimics.

Sancho-Vaello, E.Gil-Carton, D.Francois, P.Bonetti, E.J.Kreir, M.Pothula, K.R.Kleinekathofer, U.Zeth, K.

(2020) Sci Rep 10: 17356-17356

  • DOI: https://doi.org/10.1038/s41598-020-74401-5
  • Primary Citation of Related Structures:  
    7PDC

  • PubMed Abstract: 

    The human cathelicidin LL-37 serves a critical role in the innate immune system defending bacterial infections. LL-37 can interact with molecules of the cell wall and perforate cytoplasmic membranes resulting in bacterial cell death. To test the interactions of LL-37 and bacterial cell wall components we crystallized LL-37 in the presence of detergents and obtained the structure of a narrow tetrameric channel with a strongly charged core. The formation of a tetramer was further studied by cross-linking in the presence of detergents and lipids. Using planar lipid membranes a small but defined conductivity of this channel could be demonstrated. Molecular dynamic simulations underline the stability of this channel in membranes and demonstrate pathways for the passage of water molecules. Time lapse studies of E. coli cells treated with LL-37 show membrane discontinuities in the outer membrane followed by cell wall damage and cell death. Collectively, our results open a venue to the understanding of a novel AMP killing mechanism and allows the rational design of LL-37 derivatives with enhanced bactericidal activity.


  • Organizational Affiliation

    Unidad de Biofisica, Centro Mixto Consejo Superior de Investigaciones Cientificas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC, UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cathelicidin antimicrobial peptide
A, B
37Homo sapiensMutation(s): 0 
Gene Names: CAMPCAP18FALL39HSD26
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P49913 (Homo sapiens)
Explore P49913 
Go to UniProtKB:  P49913
PHAROS:  P49913
GTEx:  ENSG00000164047 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49913
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
C [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.1α = 90
b = 51.42β = 106.36
c = 26.22γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2021-11-03
    Changes: Data collection
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description