6GS3

Crystal Structure of the Uperin-3.5 peptide from Uperoleia mjobergii forming cross-alpha fibril


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The amphibian antimicrobial peptide uperin 3.5 is a cross-alpha /cross-beta chameleon functional amyloid.

Salinas, N.Tayeb-Fligelman, E.Sammito, M.D.Bloch, D.Jelinek, R.Noy, D.Uson, I.Landau, M.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: 10.1073/pnas.2014442118
  • Primary Citation of Related Structures:  
    6GS3

  • PubMed Abstract: 
  • Antimicrobial activity is being increasingly linked to amyloid fibril formation, suggesting physiological roles for some human amyloids, which have historically been viewed as strictly pathological agents. This work reports on formation of functional cross-α amyloid fibrils of the amphibian antimicrobial peptide uperin 3 ...

    Antimicrobial activity is being increasingly linked to amyloid fibril formation, suggesting physiological roles for some human amyloids, which have historically been viewed as strictly pathological agents. This work reports on formation of functional cross-α amyloid fibrils of the amphibian antimicrobial peptide uperin 3.5 at atomic resolution, an architecture initially discovered in the bacterial PSMα3 cytotoxin. The fibrils of uperin 3.5 and PSMα3 comprised antiparallel and parallel helical sheets, respectively, recapitulating properties of β-sheets. Uperin 3.5 demonstrated chameleon properties of a secondary structure switch, forming mostly cross-β fibrils in the absence of lipids. Uperin 3.5 helical fibril formation was largely induced by, and formed on, bacterial cells or membrane mimetics, and led to membrane damage and cell death. These findings suggest a regulation mechanism, which includes storage of inactive peptides as well as environmentally induced activation of uperin 3.5, via chameleon cross-α/β amyloid fibrils.


    Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), 22607 Hamburg, Germany.



Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uperin-3.5A, B17Uperoleia mjobergiiMutation(s): 0 
UniProt
Find proteins for P82042 (Uperoleia mjobergii)
Explore P82042 
Go to UniProtKB:  P82042
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP82042
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download Ideal Coordinates CCD File 
C [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
D [auth B],
E [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 19.7α = 90
b = 28.44β = 106.95
c = 20.32γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Arcimboldophasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Data collection
  • Version 1.2: 2021-01-13
    Changes: Database references, Derived calculations
  • Version 1.3: 2021-01-20
    Changes: Database references