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- PDB-9rfv: Cryo-EM structure of amyloidogenic antimicrobial peptide aurein 1... -

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Basic information

Entry
Database: PDB / ID: 9rfv
TitleCryo-EM structure of amyloidogenic antimicrobial peptide aurein 1.2 polymorph 2 in aqueous solution
Components(Aurein-1.2) x 2
KeywordsANTIMICROBIAL PROTEIN / Amyloid / Antimicrobial
Function / homologyAurein antibiotic peptide family / Aurein-like antibiotic peptide / defense response to bacterium / extracellular region / Aurein-1.2
Function and homology information
Biological speciesRanoidea aurea (green and golden bell frog)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsRagonis-Bachar, P. / Strati, F. / Gustavsson, E. / Khokhlov, A. / Barnea, E. / Rayan, B. / Upchr, A. / Landau, M. / Banerjee, S.
Funding supportEuropean Union, Israel, Germany, 8items
OrganizationGrant numberCountry
European Research Council (ERC)101087140European Union
Israel Science Foundation2111/20 Israel
Volkswagen Foundation76251-4659/2022 (ZN 4042) Germany
German Research Foundation (DFG)152/772-1 Germany
German Research Foundation (DFG)152/774-1 Germany
German Research Foundation (DFG)152/775-1 Germany
German Research Foundation (DFG)152/776-1 Germany
German Research Foundation (DFG)152/777-1 FUGG Germany
CitationJournal: To Be Published
Title: Amyloidogenic Nature and Structural Polymorphism of Antimicrobial, Virulent and Defense Peptides
Authors: Ragonis-Bachar, P. / Strati, F. / Gustavsson, E. / Khokhlov, A. / Barnea, E. / Rayan, B. / Upchr, A. / Landau, M. / Banerjee, S.
History
DepositionJun 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurein-1.2
B: Aurein-1.2
C: Aurein-1.2
D: Aurein-1.2
E: Aurein-1.2
F: Aurein-1.2
G: Aurein-1.2
H: Aurein-1.2
I: Aurein-1.2
J: Aurein-1.2
K: Aurein-1.2
L: Aurein-1.2


Theoretical massNumber of molelcules
Total (without water)14,40212
Polymers14,40212
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide
Aurein-1.2


Mass: 1163.387 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ranoidea aurea (green and golden bell frog)
Production host: Ranoidea aurea (green and golden bell frog)
References: UniProt: P82387
#2: Protein/peptide Aurein-1.2


Mass: 1310.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ranoidea aurea (green and golden bell frog)
Production host: Ranoidea aurea (green and golden bell frog)
References: UniProt: P82387
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Aurein 1.2 / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Ranoidea aurea (green and golden bell frog)
Buffer solutionpH: 5.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was fibrillated in aqueous solution
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9.8.92model fitting
9Servalcatmodel refinement
10RELION4initial Euler assignment
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -2.4 ° / Axial rise/subunit: 4.84 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 131027
3D reconstructionResolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90810 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingDetails: De novo generated in Coot / Source name: Other / Type: other

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