6S6M | pdb_00006s6m

Crystal structure of the human LL37(17-29) antimicrobial peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.268 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6S6M

This is version 1.1 of the entry. See complete history

Literature

The Human LL-37(17-29) antimicrobial peptide reveals a functional supramolecular structure.

Engelberg, Y.Landau, M.

(2020) Nat Commun 11: 3894-3894

  • DOI: https://doi.org/10.1038/s41467-020-17736-x
  • Primary Citation Related Structures: 
    6S6M, 6S6N

  • PubMed Abstract: 

    Here, we demonstrate the self-assembly of the antimicrobial human LL-37 active core (residues 17-29) into a protein fibril of densely packed helices. The surface of the fibril encompasses alternating hydrophobic and positively charged zigzagged belts, which likely underlie interactions with and subsequent disruption of negatively charged lipid bilayers, such as bacterial membranes. LL-37 17-29 correspondingly forms wide, ribbon-like, thermostable fibrils in solution, which co-localize with bacterial cells. Structure-guided mutagenesis analyses supports the role of self-assembly in antibacterial activity. LL-37 17-29 resembles, in sequence and in the ability to form amphipathic helical fibrils, the bacterial cytotoxic PSMα3 peptide that assembles into cross-α amyloid fibrils. This argues helical, self-assembling, basic building blocks across kingdoms of life and points to potential structural mimicry mechanisms. The findings expose a protein fibril which performs a biological activity, and offer a scaffold for functional and durable biomaterials for a wide range of medical and technological applications.


  • Organizational Affiliation
    • Department of Biology, Technion-Israel Institute of Technology, 3200003, Haifa, Israel.

Macromolecule Content 

  • Total Structure Weight: 3.45 kDa 
  • Atom Count: 300 
  • Modeled Residue Count: 26 
  • Deposited Residue Count: 26 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cathelicidin antimicrobial peptide
A, B
13Homo sapiensMutation(s): 0 
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.268 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.45α = 90
b = 41.45β = 90
c = 57.47γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references