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- EMDB-53942: Cryo-EM structure of amyloidogenic antimicrobial peptide aurein 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-53942
TitleCryo-EM structure of amyloidogenic antimicrobial peptide aurein 1.2 polymorph 2 in aqueous solution
Map data
Sample
  • Complex: Aurein 1.2
    • Protein or peptide: Aurein-1.2
  • Protein or peptide: Aurein-1.2
KeywordsAmyloid / Antimicrobial / ANTIMICROBIAL PROTEIN
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)
Methodhelical 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, 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 / Banerjee S
History
DepositionJun 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_53942.png

Downloads & links

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Map

FileDownload / File: emd_53942.map.gz / Format: CCP4 / Size: 59.6 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 250 pix.
= 208. Å		0.83 Å/pix.
x 250 pix.
= 208. Å		0.83 Å/pix.
x 250 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00554
Minimum - Maximum-0.020574866 - 0.03351559
Average (Standard dev.)0.0000795511 (±0.0016222094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53942_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53942_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Aurein 1.2

EntireName: Aurein 1.2
Components
  • Complex: Aurein 1.2
    • Protein or peptide: Aurein-1.2
  • Protein or peptide: Aurein-1.2

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Supramolecule #1: Aurein 1.2

SupramoleculeName: Aurein 1.2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Ranoidea aurea (green and golden bell frog)

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Macromolecule #1: Aurein-1.2

MacromoleculeName: Aurein-1.2 / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Ranoidea aurea (green and golden bell frog)
Molecular weightTheoretical: 1.163387 KDa
Recombinant expressionOrganism: Ranoidea aurea (green and golden bell frog)
SequenceString:
DIIKKIAESF (NH2)

UniProtKB: Aurein-1.2

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Macromolecule #2: Aurein-1.2

MacromoleculeName: Aurein-1.2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ranoidea aurea (green and golden bell frog)
Molecular weightTheoretical: 1.310561 KDa
Recombinant expressionOrganism: Ranoidea aurea (green and golden bell frog)
SequenceString:
FDIIKKIAES F(NH2)

UniProtKB: Aurein-1.2

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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: 5.5
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was fibrillated in aqueous solution

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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: 3.5 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: 4.84 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.40 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 90810
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 131027 / 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. 4)
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-9rfv:
Cryo-EM structure of amyloidogenic antimicrobial peptide aurein 1.2 polymorph 2 in aqueous solution

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