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- EMDB-45610: Cryo-EM of CarbIF tube -

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Basic information

Entry
Database: EMDB / ID: EMD-45610
TitleCryo-EM of CarbIF tube
Map data
Sample
  • Complex: CarbIF tubular micelle
Keywordsdipeptides / micelle / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 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: Faraday Discuss / Year: 2025
Title: Cryo-EM for atomic characterization of supramolecular gels.
Authors: Ravi R Sonani / Simona Bianco / Mark A B Kreutzberger / Dave J Adams / Edward H Egelman /
Abstract: While there have been great advances in the design and synthesis of supramolecular gels, their characterization methods have largely stayed the same, with electron microscopy of dried samples, or ...While there have been great advances in the design and synthesis of supramolecular gels, their characterization methods have largely stayed the same, with electron microscopy of dried samples, or small-angle scattering and spectroscopy dominating the approaches used. Although these methods provide valuable insights into structural properties, they are unable to unambiguously generate reliable atomic models that can further guide the site-specific modification of supramolecular gelators. Cryogenic electron microscopy (cryo-EM), allowing the high-resolution imaging of the sample in a hydrated state, has emerged as the dominant technique in structural biology, but has yet to become a routine method in materials science. Here, we describe the use of cryo-EM to determine the atomic structure of the tubular micelle formed by the dipeptide CarbIF, revealing the mechanism of assembly and gelation. Using the CarbIF micelle as an example, we highlight some of the challenges in using cryo-EM to study such materials, and how determination of the helical symmetry can be the most difficult aspect of such a project.
History
DepositionJul 2, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45610.png

Downloads & links

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Map

FileDownload / File: emd_45610.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.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-0.11751194 - 15.617528
Average (Standard dev.)0.142329 (±1.0437877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45610_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_45610_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CarbIF tubular micelle

EntireName: CarbIF tubular micelle
Components
  • Complex: CarbIF tubular micelle

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Supramolecule #1: CarbIF tubular micelle

SupramoleculeName: CarbIF tubular micelle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

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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: 0.692 Å
Applied symmetry - Helical parameters - Δ&Phi: 153.94 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1516102
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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