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- EMDB-26962: Cryo-EM of self-assembling compound pBP-NBD -

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Basic information

Entry
Database: EMDB / ID: EMD-26962
TitleCryo-EM of self-assembling compound pBP-NBD
Map dataCryo-EM of compound nanotube pBP-NBD
Sample
  • Complex: compound pBP-NBD
Keywordscompound / nanofibers / self-assembly filament / TOXIN
Biological speciessynthetic construct (others)
Methodhelical reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsWang F / Yi M / Xu B / Egelman EH
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA142746 United States
National Science Foundation (NSF, United States)DMR-2011846 United States
CitationJournal: J Am Chem Soc / Year: 2022
Title: Enzyme Responsive Rigid-Rod Aromatics Target "Undruggable" Phosphatases to Kill Cancer Cells in a Mimetic Bone Microenvironment.
Authors: Meihui Yi / Fengbin Wang / Weiyi Tan / Jer-Tsong Hsieh / Edward H Egelman / Bing Xu /
Abstract: Bone metastasis remains a challenge in cancer treatment. Here we show enzymatic responsive rigid-rod aromatics acting as the substrates of "undruggable" phosphatases to kill cancer cells in a mimetic ...Bone metastasis remains a challenge in cancer treatment. Here we show enzymatic responsive rigid-rod aromatics acting as the substrates of "undruggable" phosphatases to kill cancer cells in a mimetic bone microenvironment. By phosphorylation and conjugating nitrobenzoxadiazole (NBD) to hydroxybiphenylcarboxylate (BP), we obtained pBP-NBD () as a substrate of both acid and alkaline phosphatases. effectively kills both metastatic castration-resistant prostate cancer cells (mCRPCs) and osteoblast mimic cells in their coculture. enters Saos2 almost instantly to target the endoplasmic reticulum (ER) of the cells. Co-culturing with Saos2 cells boosts the cellular uptake of by mCRPCs. Cryo-EM reveals the nanotube structures of both (2.4 Å resolution, pH 5.6) and (2.2 Å resolution, pH 7.4). The helical packing of both nanotubes is identical, held together by strong pi-stacking interactions. Besides reporting the atomistic structure of nanotubes formed by the assembly of rigid-rod aromatics, this work expands the pool of molecules for designing EISA substrates that selectively target TME.
History
DepositionMay 12, 2022-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26962.png

Downloads & links

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Map

FileDownload / File: emd_26962.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of compound nanotube pBP-NBD
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: 0.38
Minimum - Maximum-0.5516905 - 1.1550341
Average (Standard dev.)0.0038226151 (±0.04114164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
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: half A

Fileemd_26962_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_26962_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : compound pBP-NBD

EntireName: compound pBP-NBD
Components
  • Complex: compound pBP-NBD

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Supramolecule #1: compound pBP-NBD

SupramoleculeName: compound pBP-NBD / type: complex / ID: 1 / Parent: 0
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: 5.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.35 Å
Applied symmetry - Helical parameters - Δ&Phi: 16.35 °
Applied symmetry - Helical parameters - Axial symmetry: C7 (7 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 889335
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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