Chen Sun

Chen Sun

she/her

Structural Biologist | Cryo-EM | Cryo-ET | Cell Therapy & Drug Discovery | Deciphering molecular structures to drive therapeutic innovation

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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.

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Posts

Ctffind3

less than 1 minute read

Published:

Run CTFFIND3 with Multiple CPUs

Centrifugation Types and Tips

3 minute read

Published:

There are two main types of centrifugation: differential centrifugation and density gradient centrifugation. Differential pelleting is commonly used to pellet cells, bacteria, and other large particles based on differences in mass, density and shape.

Aquilos Cryo-FIB milling protocol

3 minute read

Published:

Step 1: Initial Setup

  • Write down chamber pressure.
  • Fill liquid nitrogen to the tank.
  • Cool down the heat exchanger.
  • Set Nâ‚‚ gas flow rate to 180 mg/s.

How to run relion on Herman cluster?

1 minute read

Published:

I’m sharing a SLURM submission script that’s tailored for running RELION on Herman cluster. While an interactive session can be helpful for initial testing, debugging, and code troubleshooting, it’s recommended to utilize the full potential of the cluster by submitting jobs through the SLURM system using the sbatch command.

What Does Fourier Transform Do to Cryo-EM Images?

1 minute read

Published:

Cryo-EM images are formed by pixels with different intensity in grayscale. Each pixel is represented as a number in the image file. Below is a table simulating the pixel intensity of an image.

Amyloid processing tips

2 minute read

Published:

  1. Amyloid Atlas https://people.mbi.ucla.edu/sawaya/amyloidatlas/

Good box size for image processing

1 minute read

Published:

Criteria for good image size:

  1. even number (and divisible by 4)
  2. largest prime number factor is small (<=7) to make FFT faster
    List of good numbers (<=2000):
    All: [16, 20, 24, 28, 32, 36, 40, 48, 56, 60, 64, 72, 80, 84, 96, 100, 108, 112, 120, 128, 140, 144, 160, 168, 180, 192, 196, 200, 216, 224, 240, 252, 256, 280, 288, 300, 320, 324, 336, 360, 384, 392, 400, 420, 432, 448, 480, 500, 504, 512, 540, 560, 576, 588, 600, 640, 648, 672, 700, 720, 756, 768, 784, 800, 840, 864, 896, 900, 960, 972, 980, 1000, 1008, 1024, 1080, 1120, 1152, 1176, 1200, 1260, 1280, 1296, 1344, 1372, 1400, 1440, 1500, 1512, 1536, 1568, 1600, 1620, 1680, 1728, 1764, 1792, 1800, 1920, 1944, 1960, 2000]
    2: [16, 32, 64, 128, 256, 512, 1024]
    3: [24, 36, 48, 72, 96, 108, 144, 192, 216, 288, 324, 384, 432, 576, 648, 768, 864, 972, 1152, 1296, 1536, 1728, 1944]
    5: [20, 40, 60, 80, 100, 120, 160, 180, 200, 240, 300, 320, 360, 400, 480, 500, 540, 600, 640, 720, 800, 900, 960, 1000, 1080, 1200, 1280, 1440, 1500, 1600, 1620, 1800, 1920, 2000]
    7: [28, 56, 84, 112, 140, 168, 196, 224, 252, 280, 336, 392, 420, 448, 504, 560, 588, 672, 700, 756, 784, 840, 896, 980, 1008, 1120, 1176, 1260, 1344, 1372, 1400, 1512, 1568, 1680, 1764, 1792, 1960]

What is the Preferred Orientation Problem?

2 minute read

Published:

Preferred orientation occurs when most of the particles present the same view in the EM image. This has been a persistent issue for high-resolution structure determination with cryo-EM, especially for asymmetric samples. It is typically caused by the adherence of the sample to the air-water interface or to the substrate of the grid (e.g., carbon film or graphene oxide).

EMpapers

Posters

portfolio

publications

Bioengineered Norovirus S60 Nanoparticles as a Multifunctional Vaccine Platform

Published in ACS Nano, 2018

This study presents a bioengineered S60 nanoparticle derived from Norovirus as a versatile vaccine platform capable of displaying various antigens.

Recommended citation: Xia M, Huang P, Sun C, Han L, Vago FS, Li K, Zhong W, Jiang W, Klassen JS, Jiang X, Tan M. (2018). "Bioengineered Norovirus S60 Nanoparticles as a Multifunctional Vaccine Platform." ACS Nano. 12(11):10665–10682. https://doi.org/10.1021/acsnano.8b02776
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Sub-3 Ă… Apoferritin Structure Determined With Full Range of Phase Shifts Using A Single Position Of Volta Phase Plate

Published in Journal of Structural Biology, 2019

In this study, we evaluated the feasibility of using a single position on the Volta Phase Plate (VPP) and examined its impact on image quality and phase shift distribution. Two cryo-EM datasets were collected—one with phase shifts ranging from 0–180°, and another extending to 0–360°. Both datasets yielded high-resolution reconstructions of apoferritin. Our results demonstrate that images with large phase shifts remain suitable for high-resolution structure determination, highlighting the robustness and flexibility of VPP imaging strategies.

Recommended citation: Kunpeng Li, Chen Sun, Thomas Klose, Frank S. Vago, Jose Irimia-Dominguez, Ruben Vidal, Wen Jiang. (2019). "Sub-3 Å Apoferritin Structure Determined With Full Range of Phase Shifts Using A Single Position Of Volta Phase Plate." Journal of Structural Biology. 206(2), pp. 225–232.
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Cryo-EM Structure of Heterologous Protein Complex Loaded Thermotoga Maritima Encapsulin Capsid

Published in Biomolecules, 2020

This study reports the cryo-EM structure of Thermotoga maritima encapsulin loaded with a heterologous protein complex, providing insight into capsid architecture and protein cargo encapsulation.

Recommended citation: Xiong, Xiansong*, Chen Sun*, Frank S. Vago, Thomas Klose, Jiankang Zhu, and Wen Jiang. (2020). "Cryo-EM Structure of Heterologous Protein Complex Loaded Thermotoga Maritima Encapsulin Capsid." Biomolecules. 10(9): 1342.
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High resolution single particle Cryo-EM refinement using JSPR

Published in Progress in Biophysics and Molecular Biology, 2021

This paper introduces JSPR, a cryo-EM refinement tool that enhances single particle resolution through improved real-space alignment and classification strategies.

Recommended citation: Chen Sun, Brenda Gonzalez, Frank S. Vago, and Wen Jiang. (2021). "High resolution single particle Cryo-EM refinement using JSPR." Progress in Biophysics and Molecular Biology. 160: 37–42.
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Helical Indexing in Real Space

Published in Scientific Reports, 2022

A user-friendly web interface for automatically determining helical parameters from an initial model in real space.

Recommended citation: Chen Sun, Brenda Gonzalez, Wen Jiang. (2022). "Helical Indexing in Real Space." Scientific Reports. 12, 8162.
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Structural diversity of axonemes across mammalian motile cilia

Published in Nature, 2025

This study reveals the structural heterogeneity of mammalian axonemes using cryo-EM, offering insights into tissue-specific ciliary architecture.

Recommended citation: Leung MR, Chen Sun, Zeng J, Anderson JR, Niu Q, Huang W, Noteborn WEM, Brown A, Zeev-Ben-Mordehai T, Zhang R. (2025). "Structural diversity of axonemes across mammalian motile cilia." Nature. 637(8048):1170–1177. https://doi.org/10.1038/s41586-024-08337-5
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Human endogenous retrovirus K (HERV‑K) envelope structures in pre‑ and post‑fusion states

Published in Science Advances, 2025

Cryo‑EM structures of HERV‑K envelope in both pre‑ and post‑fusion conformations complexed with novel monoclonal antibodies. Read the press release

Recommended citation: Jeremy Shek et al. ,Human endogenous retrovirus K (HERV-K) envelope structures in pre- and postfusion by cryo-EM.Sci. Adv.11,eady8168(2025).DOI:10.1126/sciadv.ady8168
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talks

teaching

Human anatomy and physiology BIOL 203/204

Undergraduate course, Purdue University, Department of Biological Sciences, 2017

Served as a teaching assistant for lab sessions. Responsibilities include collaborating with fellow teaching assistants to deliver lab presentations, preparing the required materials, and providing guidance to students.