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- EMDB-44636: Cryo-EM of Azo-ffspy fiber -

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Basic information

Entry
Database: EMDB / ID: EMD-44636
TitleCryo-EM of Azo-ffspy fiber
Map datacryo-EM map of Azo-ffspy
Sample
  • Complex: ffspy fiber
    • Protein or peptide: D-peptide ffspy
KeywordsD-peptide / peptide-fiber / helical / PROTEIN FIBRIL
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZia A / Guo J / Xu B / Wang F
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA142746 United States
CitationJournal: J Am Chem Soc / Year: 2024
Title: Cell-Free Nonequilibrium Assembly for Hierarchical Protein/Peptide Nanopillars.
Authors: Jiaqi Guo / Ayisha Zia / Qianfeng Qiu / Michael Norton / Kangqiang Qiu / Junichi Usuba / Zhiyu Liu / Meihui Yi / Shane T Rich-New / Michael Hagan / Seth Fraden / Grace D Han / Jiajie Diao / ...Authors: Jiaqi Guo / Ayisha Zia / Qianfeng Qiu / Michael Norton / Kangqiang Qiu / Junichi Usuba / Zhiyu Liu / Meihui Yi / Shane T Rich-New / Michael Hagan / Seth Fraden / Grace D Han / Jiajie Diao / Fengbin Wang / Bing Xu /
Abstract: Cells contain intricate protein nanostructures, but replicating them outside of cells presents challenges. One such example is the vertical fibronectin pillars observed in embryos. Here, we ...Cells contain intricate protein nanostructures, but replicating them outside of cells presents challenges. One such example is the vertical fibronectin pillars observed in embryos. Here, we demonstrate the creation of cell-free vertical fibronectin pillar mimics using nonequilibrium self-assembly. Our approach utilizes enzyme-responsive phosphopeptides that assemble into nanotubes. Enzyme action triggers shape changes in peptide assemblies, driving the vertical growth of protein nanopillars into bundles. These bundles, with peptide nanotubes serving as a template to remodel fibronectin, can then recruit collagen, which forms aggregates or bundles depending on their types. Nanopillar formation relies on enzyme-catalyzed nonequilibrium self-assembly and is governed by the concentrations of enzyme, protein, peptide, the structure of the peptide, and peptide assembly morphologies. Cryo-EM reveals unexpected nanotube thinning and packing after dephosphorylation, indicating a complex sculpting process during assembly. Our study demonstrates a cell-free method for constructing intricate, multiprotein nanostructures with directionality and composition.
History
DepositionApr 25, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44636.png

Downloads & links

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Map

FileDownload / File: emd_44636.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of Azo-ffspy
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.289
Minimum - Maximum-0.3845521 - 1.0701022
Average (Standard dev.)0.0024141776 (±0.034595437)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half B

Fileemd_44636_half_map_1.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_44636_half_map_2.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ffspy fiber

EntireName: ffspy fiber
Components
  • Complex: ffspy fiber
    • Protein or peptide: D-peptide ffspy

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Supramolecule #1: ffspy fiber

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

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Macromolecule #1: D-peptide ffspy

MacromoleculeName: D-peptide ffspy / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: DEXTRO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 850.809 Da
SequenceString:
(A1APX)(DPN)(DPN)(DSN)(A1AP1)

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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

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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.162 Å
Applied symmetry - Helical parameters - Δ&Phi: 46.520 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 887952
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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