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- EMDB-54647: Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin... -

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Basic information

Entry
Database: EMDB / ID: EMD-54647
TitleCryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 2 in PBS pH 6.5
Map data
Sample
  • Complex: Brevinin-1OKc
    • Protein or peptide: Brevinin-1OKc
KeywordsAmyloid / Antimicrobial / ANTIMICROBIAL PROTEIN
Function / homologykilling of cells of another organism / defense response to Gram-positive bacterium / AbyA5
Function and homology information
Biological speciesNidirana okinavana (Kampira Falls frog)
Methodhelical reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsRagonis-Bachar P / Strati F / Gustavsson E / Khokhlov A / Barnea E / Rayan B / Upchr A / Landau M
Funding supportEuropean Union, Israel, Germany, 8 items
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, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54647.png

Downloads & links

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Map

FileDownload / File: emd_54647.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.00821409 - 0.02179893
Average (Standard dev.)0.000038100134 (±0.0011329929)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54647_msk_1.map
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Additional map: #2

Fileemd_54647_additional_1.map
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Additional map: #1

Fileemd_54647_additional_2.map
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Half map: #2

Fileemd_54647_half_map_1.map
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Half map: #1

Fileemd_54647_half_map_2.map
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Sample components

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Entire : Brevinin-1OKc

EntireName: Brevinin-1OKc
Components
  • Complex: Brevinin-1OKc
    • Protein or peptide: Brevinin-1OKc

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Supramolecule #1: Brevinin-1OKc

SupramoleculeName: Brevinin-1OKc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nidirana okinavana (Kampira Falls frog)

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Macromolecule #1: Brevinin-1OKc

MacromoleculeName: Brevinin-1OKc / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Nidirana okinavana (Kampira Falls frog)
Molecular weightTheoretical: 2.274832 KDa
SequenceString:
FFGSIIGALA KGLPSLISLI KK(NH2)

UniProtKB: AbyA5

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.5 / Details: 1xPBS pH 6.5 from Sigma Aldrich
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was fibrillated in PBS pH 6.5

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 59.5 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 312286
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 328282 / Software - Name: Topaz
Startup modelType of model: OTHER
Details: Relion initial model generation script: relion_helix_inimodel2d
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: De novo generated in Coot
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9s7q:
Cryo-EM structure of amyloidogenic antimicrobial peptide Brevinin-1OKc polymorph 2 in PBS pH 6.5

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