Sub-3 Å apoferritin structure determined with full range of phase shifts using a single position of volta phase plate

Kunpeng Li, Chen Sun, Thomas Klose, Jose Irimia-Dominguez, Frank S. Vago, Ruben Vidal, Wen Jiang

Research output: Contribution to journalArticle

Abstract

Volta Phase Plate (VPP) has become an invaluable tool for cryo-EM structural determination of small protein complexes by increasing image contrast. Currently, the standard protocol of VPP usage periodically changes the VPP position to a fresh spot during data collection. Such a protocol was to target the phase shifts to a relatively narrow range (around 90°) based on the observations of increased phase shifts and image blur associated with more images taken with a single VPP position. Here, we report a 2.87 Å resolution structure of apoferritin reconstructed from a dataset collected using only a single position of VPP. The reconstruction resolution and map density features are nearly identical to the reconstruction from the control dataset collected with periodic change of VPP positions. Further experiments have verified that similar results, including a 2.5 Å resolution structure, could be obtained with a full range of phase shifts, different spots of variable phase shift increasing rates, and at different ages of the VPP post-installation. Furthermore, we have found that the phase shifts at low resolutions, probably related to the finite size of the Volta spots, could not be correctly modeled by current CTF model using a constant phase shift at all frequencies. In dataset III, severe beam tilt issue was identified but could be computationally corrected with iterative refinements. The observations in this study may provide new insights into further improvement of both the efficiency and robustness of VPP, and to help turn VPP into a plug-and-play device for high-resolution cryo-EM.

Original languageEnglish (US)
JournalJournal of Structural Biology
DOIs
StatePublished - Jan 1 2019

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Apoferritins
Equipment and Supplies
Datasets
Proteins

Keywords

  • Apoferritin
  • Beam tilt
  • Cryo-EM
  • Near-atomic resolution
  • Phase shift
  • Volta phase plate

ASJC Scopus subject areas

  • Structural Biology

Cite this

Sub-3 Å apoferritin structure determined with full range of phase shifts using a single position of volta phase plate. / Li, Kunpeng; Sun, Chen; Klose, Thomas; Irimia-Dominguez, Jose; Vago, Frank S.; Vidal, Ruben; Jiang, Wen.

In: Journal of Structural Biology, 01.01.2019.

Research output: Contribution to journalArticle

Li, Kunpeng ; Sun, Chen ; Klose, Thomas ; Irimia-Dominguez, Jose ; Vago, Frank S. ; Vidal, Ruben ; Jiang, Wen. / Sub-3 Å apoferritin structure determined with full range of phase shifts using a single position of volta phase plate. In: Journal of Structural Biology. 2019.
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abstract = "Volta Phase Plate (VPP) has become an invaluable tool for cryo-EM structural determination of small protein complexes by increasing image contrast. Currently, the standard protocol of VPP usage periodically changes the VPP position to a fresh spot during data collection. Such a protocol was to target the phase shifts to a relatively narrow range (around 90°) based on the observations of increased phase shifts and image blur associated with more images taken with a single VPP position. Here, we report a 2.87 {\AA} resolution structure of apoferritin reconstructed from a dataset collected using only a single position of VPP. The reconstruction resolution and map density features are nearly identical to the reconstruction from the control dataset collected with periodic change of VPP positions. Further experiments have verified that similar results, including a 2.5 {\AA} resolution structure, could be obtained with a full range of phase shifts, different spots of variable phase shift increasing rates, and at different ages of the VPP post-installation. Furthermore, we have found that the phase shifts at low resolutions, probably related to the finite size of the Volta spots, could not be correctly modeled by current CTF model using a constant phase shift at all frequencies. In dataset III, severe beam tilt issue was identified but could be computationally corrected with iterative refinements. The observations in this study may provide new insights into further improvement of both the efficiency and robustness of VPP, and to help turn VPP into a plug-and-play device for high-resolution cryo-EM.",
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AU - Vago, Frank S.

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