9HPP | pdb_00009hpp

Helical form of Citropin 1.3

• PDB DOI: https://doi.org/10.2210/pdb9HPP/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Dryopsophus citropa
• Mutation(s): No 


• Deposited: 2024-12-13 Released: 2025-10-08 
• Deposition Author(s): Bloch, Y., Rayan, B., Landau, M.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission, Israel Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.323 (Depositor), 0.329 (DCC) 
• R-Value Work: 
  0.284 (Depositor), 0.288 (DCC) 
• R-Value Observed: 
  0.288 (Depositor) 

Starting Models: experimental

Literature

Structural and Functional Versatility of the Amyloidogenic Non-Amidated Variant of the Antimicrobial Peptide Citropin 1.3.

Strati, F., Cali, M.P., Bloch, Y., Mostafavi, S., Monistrol, J., Golubev, A., Rayan, B., Gustavsson, E., Landau, M.

(2025) Adv Sci (Weinh) 12: e03997-e03997

• PubMed: 41016026 
• DOI: https://doi.org/10.1002/advs.202503997
• Primary Citation Related Structures: 
  9HGB, 9HGL, 9HGT, 9HI8, 9HID, 9HPP


• PubMed Abstract: 
  

  Citropin 1.3 is an antimicrobial peptide secreted by the amphibian Litoria citropa (Southern bell frog). In this study, the structural and functional properties of its non-amidated form, which self-assembles into distinct fibrillar architectures, are investigated. Using cryogenic electron microscopy, X-ray crystallography, and fluorescence microscopy with model membranes and cells, diverse supramolecular structures, including canonical amyloid fibrils, multilayered nanotubes, and a novel mixed fibril type, are identified. In giant unilamellar vesicles, citropin 1.3 promoted membrane fusion and underwent lipid-induced phase separation. In mammalian cells, it permeabilized membranes, induced cell death, and colocalized with nucleic acids. These findings link antimicrobial activity to amyloid assembly and highlight the peptide's structural plasticity and potential biological functions, offering new insights into amyloid-based antimicrobial mechanisms.

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Organizational Affiliation: 
• CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, 22603, Hamburg, Germany.
European Molecular Biology Laboratory (EMBL), 22607, Hamburg, Germany.
Department of Biology, Technion-Israel Institute of Technology, Technion City, Haifa, 3200003, Israel.
The Center for Experimental Medicine, Universitätsklinikum Hamburg-Eppendorf (UKE), 20251, Hamburg, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.26 kDa 
• Atom Count: 248 
• Modeled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citropin-1.3	A, B	16	Dryopsophus citropa	Mutation(s): 0
UniProt
Find proteins for P81846 (Ranoidea citropa) Explore P81846  Go to UniProtKB:  P81846

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.323 (Depositor), 0.329 (DCC) 
• R-Value Work:  0.284 (Depositor), 0.288 (DCC) 
• R-Value Observed: 0.288 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.83	α = 90
b = 67.83	β = 90
c = 67.83	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Bloch, Y., Rayan, B., Landau, M.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	945405
Israel Science Foundation	Israel	2111/20

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release
  
• Version 1.1: 2025-12-24
  Changes: Database references