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- PDB-9s7o: Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin... -

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Basic information

Entry
Database: PDB / ID: 9s7o
TitleCryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 1 in water
ComponentsBrevinin-1OKc
KeywordsANTIMICROBIAL PROTEIN / Amyloid / Antimicrobial
Function / homologykilling of cells of another organism / defense response to Gram-positive bacterium / AbyA5
Function and homology information
Biological speciesNidirana okinavana (Kampira Falls frog)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsRagonis-Bachar, P. / Strati, F. / Gustavsson, E. / Khokhlov, A. / Barnea, E. / Rayan, B. / Upchr, A. / Landau, M.
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.
History
DepositionAug 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

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Assembly

Deposited unit
A: Brevinin-1OKc
B: Brevinin-1OKc
C: Brevinin-1OKc
D: Brevinin-1OKc
E: Brevinin-1OKc
F: Brevinin-1OKc


Theoretical massNumber of molelcules
Total (without water)13,6496
Polymers13,6496
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
Brevinin-1OKc


Mass: 2274.832 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Nidirana okinavana (Kampira Falls frog) / References: UniProt: C0HL10
Has protein modificationN

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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: Brevinin-1OKc / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Nidirana okinavana (Kampira Falls frog)
Buffer solutionpH: 7 / Details: ddH2O
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was fibrillated in ddH2O
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
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: 2000 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
1crYOLOparticle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9.8.92model fitting
9RELION5initial Euler assignment
10RELION5final Euler assignment
11RELION5classification
12RELION53D reconstruction
13Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.24 ° / Axial rise/subunit: 2.39 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 1569255
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 349067 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingDetails: De novo generated in Coot / Source name: Other / Type: other
RefinementResolution: 3.3→83.3 Å / Cor.coef. Fo:Fc: 0.656 / SU B: 42.726 / SU ML: 0.657 / ESU R: 0.814
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.63366 --
obs0.63366 15162 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 63.699 Å2
Refinement stepCycle: 1 / Total: 1430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0121450
ELECTRON MICROSCOPYr_bond_other_d00.0151590
ELECTRON MICROSCOPYr_angle_refined_deg1.3421.7281950
ELECTRON MICROSCOPYr_angle_other_deg0.4221.6723660
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.6835190
ELECTRON MICROSCOPYr_dihedral_angle_2_deg
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.04210250
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0480.2250
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.021520
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02280
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it5.6365.464790
ELECTRON MICROSCOPYr_mcbond_other5.6365.464790
ELECTRON MICROSCOPYr_mcangle_it9.6369.661970
ELECTRON MICROSCOPYr_mcangle_other9.6329.674971
ELECTRON MICROSCOPYr_scbond_it4.7397.126660
ELECTRON MICROSCOPYr_scbond_other4.7367.138661
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other9.04412.954981
ELECTRON MICROSCOPYr_long_range_B_refined15.28683657
ELECTRON MICROSCOPYr_long_range_B_other15.27868.013658
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.856 1131 -
obs--100 %

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