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- EMDB-24725: Cryo-EM reconstruction of Form1-N2 nanotube (Form I like) -

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Basic information

Entry
Database: EMDB / ID: EMD-24725
TitleCryo-EM reconstruction of Form1-N2 nanotube (Form I like)
Map dataCryo-EM of FormI-N2 nanotube
Sample
  • Complex: F1-N2 nanotube
    • Protein or peptide: F1-N2 nanotube
Keywordshelical symmetry / peptide nanotube / self-assembly / DE NOVO PROTEIN
Biological speciesSynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang F / Gnewou OM
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-DMR-1533958 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
CitationJournal: Chem Rev / Year: 2022
Title: Cryo-EM of Helical Polymers.
Authors: Fengbin Wang / Ordy Gnewou / Armin Solemanifar / Vincent P Conticello / Edward H Egelman /
Abstract: While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, ...While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.
History
DepositionAug 21, 2021-
Header (metadata) releaseSep 8, 2021-
Map releaseSep 8, 2021-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.495
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.495
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rx5
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rx5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24725.png

Downloads & links

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Map

FileDownload / File: emd_24725.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of FormI-N2 nanotube
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 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: 0.495 / Movie #1: 0.495
Minimum - Maximum-1.1747462 - 2.3319244
Average (Standard dev.)0.0033055623 (±0.06821041)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-113-15
NX/NY/NZ10616274
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-1.1752.3320.003

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Supplemental data

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Sample components

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Entire : F1-N2 nanotube

EntireName: F1-N2 nanotube
Components
  • Complex: F1-N2 nanotube
    • Protein or peptide: F1-N2 nanotube

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Supramolecule #1: F1-N2 nanotube

SupramoleculeName: F1-N2 nanotube / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synthetic construct (others)

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Macromolecule #1: F1-N2 nanotube

MacromoleculeName: F1-N2 nanotube / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synthetic construct (others)
Molecular weightTheoretical: 3.255659 KDa
SequenceString:
QAEILKADAE NNRAYARILE AHAEILKAQ

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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: 4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.112 Å
Applied symmetry - Helical parameters - Δ&Phi: -83.409 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1000000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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