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- EMDB-44190: Cryo-EM of 2NapIF tube, 10 eq. KCl -

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Basic information

Entry
Database: EMDB / ID: EMD-44190
TitleCryo-EM of 2NapIF tube, 10 eq. KCl
Map data
Sample
  • Complex: (L, L)-2NapFF micelle
Keywordsdipeptides / micelle / stereoisomers / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsSonani RR / Bianco S / Adams DJ / Egelman EH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122150 United States
CitationJournal: Matter / Year: 2025
Title: Modular salt-induced nanostructures formed by a functionalized dipeptide system
Authors: Bianco S / Sonani RR / Ghosh D / Maurya T / Bizien T / Pincham A / Smith AJ / Inoue K / Seddon A / Vassalli M / Egelman EH / Adams DJ
History
DepositionMar 21, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44190.png

Downloads & links

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Map

FileDownload / File: emd_44190.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 448 pix.
= 300.16 Å		0.67 Å/pix.
x 448 pix.
= 300.16 Å		0.67 Å/pix.
x 448 pix.
= 300.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.11819343 - 0.22648908
Average (Standard dev.)0.003347479 (±0.017193193)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 300.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened Map

Fileemd_44190_additional_1.map
AnnotationSharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44190_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44190_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 : (L, L)-2NapFF micelle

EntireName: (L, L)-2NapFF micelle
Components
  • Complex: (L, L)-2NapFF micelle

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Supramolecule #1: (L, L)-2NapFF micelle

SupramoleculeName: (L, L)-2NapFF micelle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

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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: 11
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.999 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.875 °
Applied symmetry - Helical parameters - Axial symmetry: C4 (4 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: OTHER / Number images used: 1297019
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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