[English] 日本語
Yorodumi
- PDB-9hpp: Helical form of Citropin 1.3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hpp
TitleHelical form of Citropin 1.3
ComponentsCitropin-1.3
KeywordsANTIMICROBIAL PROTEIN / frog / fibril
Function / homologyAurein antibiotic peptide family / Aurein-like antibiotic peptide / defense response to bacterium / extracellular region / Citropin-1.3
Function and homology information
Biological speciesRanoidea citropa (Blue Mountains treefrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsBloch, Y. / Rayan, B. / Landau, M.
Funding supportEuropean Union, Israel, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission945405European Union
Israel Science Foundation2111/20 Israel
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: Structural and Functional Versatility of the Amyloidogenic Non-Amidated Variant of the Antimicrobial Peptide Citropin 1.3.
Authors: Fabio Strati / Mariana Pigozzi Cali / Yehudi Bloch / Siavash Mostafavi / Jim Monistrol / Aleksandr Golubev / Bader Rayan / Emil Gustavsson / Meytal Landau /
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- ...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.
History
DepositionDec 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Citropin-1.3
B: Citropin-1.3


Theoretical massNumber of molelcules
Total (without water)3,2642
Polymers3,2642
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-6 kcal/mol
Surface area2640 Å2
Unit cell
Length a, b, c (Å)67.830, 67.830, 67.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4

-
Components

#1: Protein/peptide Citropin-1.3


Mass: 1631.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Ranoidea citropa (Blue Mountains treefrog) / References: UniProt: P81846
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 2.2
Details: 20%v/v Glycerol, 8%w/v PEG 8,000 and 8%w/v PEG 1,000. Peptide prepared in 2M acetate.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.56→47.96 Å / Num. obs: 7919 / % possible obs: 98.1 % / Redundancy: 9.56 % / Biso Wilson estimate: 29.08 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.074 / Net I/σ(I): 14.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.67-47.968.243.353660.9990.0496.1
3.31-4.679.4444.345780.9990.04398.6
1.66-1.779.621.9911760.5831.78399.6
1.56-1.666.720.9511410.332.40790.5

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
REFMAC5.8.043refinement
XDS20230630data reduction
XDS20230630data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→47.96 Å / SU ML: 0.222 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.5304
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3233 785 9.99 %
Rwork0.2839 7071 -
obs0.2878 7856 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.41 Å2
Refinement stepCycle: LAST / Resolution: 1.56→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms230 0 0 9 239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145242
X-RAY DIFFRACTIONf_angle_d1.1527327
X-RAY DIFFRACTIONf_chiral_restr0.065543
X-RAY DIFFRACTIONf_plane_restr0.007239
X-RAY DIFFRACTIONf_dihedral_angle_d17.332291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.660.38311130.37611016X-RAY DIFFRACTION87.38
1.66-1.790.36271300.29561171X-RAY DIFFRACTION99.69
1.79-1.970.30721310.27861175X-RAY DIFFRACTION100
1.97-2.250.28771300.24341189X-RAY DIFFRACTION99.92
2.25-2.840.26021360.25511216X-RAY DIFFRACTION100
2.84-47.960.351450.29781304X-RAY DIFFRACTION99.18

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more