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- EMDB-49371: Nanotube of Y5 - (5 protomer) -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-49371
TitleNanotube of Y5 - (5 protomer)
Map data
Sample
  • Complex: Synthetic nanotube
    • Protein or peptide: Y5
KeywordsPeptide nanotube / Amphiphile / Amyloids / helical / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsDas A / Conticello V
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Nanotube of Y5 - (5 promoter)
Authors: Das A / Conticello V
History
DepositionFeb 21, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49371.png

Downloads & links

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Map

FileDownload / File: emd_49371.map.gz / Format: CCP4 / Size: 316.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 436 pix.
= 366.676 Å		0.84 Å/pix.
x 436 pix.
= 366.676 Å		0.84 Å/pix.
x 436 pix.
= 366.676 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.841 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0588
Minimum - Maximum-0.10092127 - 0.29443443
Average (Standard dev.)-0.00009680483 (±0.012953329)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-218-218-218
Dimensions436436436
Spacing436436436
CellA=B=C: 366.676 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49371_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_49371_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 : Synthetic nanotube

EntireName: Synthetic nanotube
Components
  • Complex: Synthetic nanotube
    • Protein or peptide: Y5

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Supramolecule #1: Synthetic nanotube

SupramoleculeName: Synthetic nanotube / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Y5

MacromoleculeName: Y5 / type: protein_or_peptide / ID: 1 / Number of copies: 80 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 803.068 Da
SequenceString:
(ACE)KIIIYK(NH2)

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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: 3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.924 Å
Applied symmetry - Helical parameters - Δ&Phi: -3.039 °
Applied symmetry - Helical parameters - Axial symmetry: C5 (5 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64499
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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Atomic model buiding 1

RefinementOverall B value: 20.4
Output model

PDB-9nfn:
Nanotube of Y5 - (5 protomer)

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