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- PDB-9s7p: Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin... -

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Basic information

Entry
Database: PDB / ID: 9s7p
TitleCryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 1 in PBS pH 6.5
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: 2.17 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
G: Brevinin-1OKc
H: Brevinin-1OKc
I: Brevinin-1OKc
J: Brevinin-1OKc
K: Brevinin-1OKc
L: Brevinin-1OKc
A: Brevinin-1OKc
B: Brevinin-1OKc
C: Brevinin-1OKc
D: Brevinin-1OKc
E: Brevinin-1OKc
F: Brevinin-1OKc
M: Brevinin-1OKc
N: Brevinin-1OKc
O: Brevinin-1OKc
P: Brevinin-1OKc
Q: Brevinin-1OKc
R: Brevinin-1OKc


Theoretical massNumber of molelcules
Total (without water)20,23818
Polymers20,23818
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: 1124.353 Da / Num. of mol.: 18 / 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: 6.5 / Details: 1xPBS pH 6.5 from Sigma Aldrich
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was fibrillated in PBS pH 6.5
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
1Topazparticle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9.8.92model fitting
9Servalcatmodel refinement
10RELION5initial Euler assignment
11RELION5final Euler assignment
12RELION5classification
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 59.49 ° / Axial rise/subunit: 1.6 Å / Axial symmetry: C2
Particle selectionNum. of particles selected: 1523940
3D reconstructionResolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 498395 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingDetails: De novo generated in Coot / Source name: Other / Type: other
RefinementResolution: 2.17→2.17 Å / Cor.coef. Fo:Fc: 0.757 / SU B: 6.198 / SU ML: 0.137 / ESU R: 0.194
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.42971 --
obs0.42971 42654 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 57.722 Å2
Refinement stepCycle: 1 / Total: 1422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0121440
ELECTRON MICROSCOPYr_bond_other_d00.0151548
ELECTRON MICROSCOPYr_angle_refined_deg1.2421.7141890
ELECTRON MICROSCOPYr_angle_other_deg0.4711.7173528
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.1115180
ELECTRON MICROSCOPYr_dihedral_angle_2_deg
ELECTRON MICROSCOPYr_dihedral_angle_3_deg5.74610234
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0520.2216
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.021512
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02360
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_it5.0715.476774
ELECTRON MICROSCOPYr_mcbond_other5.0715.476774
ELECTRON MICROSCOPYr_mcangle_it8.8889.665936
ELECTRON MICROSCOPYr_mcangle_other8.8839.676937
ELECTRON MICROSCOPYr_scbond_it3.625.279666
ELECTRON MICROSCOPYr_scbond_other3.6175.295667
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other6.589.567955
ELECTRON MICROSCOPYr_long_range_B_refined15.49254.663706
ELECTRON MICROSCOPYr_long_range_B_other15.49254.633704
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.608 3078 -
obs--100 %

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