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- EMDB-65607: Cryo-electron microscopy structure of nanofibers formed by azoben... -

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Basic information

Entry
Database: EMDB / ID: EMD-65607
TitleCryo-electron microscopy structure of nanofibers formed by azobenzene peptides.
Map data
Sample
  • Complex: AzoPep peptide nanofibers
    • Protein or peptide: AzoPep
  • Ligand: water
Keywordsde novo protein / nanofiber
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsKawabata H / Park SY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of AzoPep peptide nanofibers
Authors: Kawabata H / Park SY
History
DepositionJul 30, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65607.png

Downloads & links

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Map

FileDownload / File: emd_65607.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 256 pix.
= 186.112 Å		0.73 Å/pix.
x 256 pix.
= 186.112 Å		0.73 Å/pix.
x 256 pix.
= 186.112 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00457
Minimum - Maximum-0.006746871 - 0.015268791
Average (Standard dev.)-0.0000074116715 (±0.00096810644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 186.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65607_msk_1.map
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AxesZYX

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Additional map: #1

Fileemd_65607_additional_1.map
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Half map: #1

Fileemd_65607_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65607_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : AzoPep peptide nanofibers

EntireName: AzoPep peptide nanofibers
Components
  • Complex: AzoPep peptide nanofibers
    • Protein or peptide: AzoPep
  • Ligand: water

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Supramolecule #1: AzoPep peptide nanofibers

SupramoleculeName: AzoPep peptide nanofibers / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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Macromolecule #1: AzoPep

MacromoleculeName: AzoPep / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.084302 KDa
Recombinant expressionOrganism: synthetic construct (others)
SequenceString:
(ACE)R(OZW)RADMR(NH2)

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 18 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.74071 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.17659 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 106867
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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