ReviewNature protocols2022
High-resolution in situ structure determination by cryo-electron tomography and subtomogram averaging using emClarity.
Review in Nature protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
59 citing papers in PubMed, 92 citations in OpenAlex.
- MxB N-Terminus Adopts a Stable α-Helix to Engage the HIV-1 Capsid Trimer Interface.bioRxiv : the preprint server for biology · 2026Article
- Graph identification of proteins in tomograms (GRIP-Tomo) 2.0: Topologically aware classification for proteins.Protein science : a publication of the Protein Society · 2026Article
- Molecular mechanism of pore formation by Plasmodium Perforin-like Protein 2.Nature communications · 2026Article
- Labeling and Localization Strategies for In Situ Cryo-Electron Tomography Across the Viral Life Cycle.Viruses · 2026Review
- Article
- Integrated experimental and AI innovations for RNA structure determination.Nature biotechnology · 2026Review
- In situ structure determination of conformationally flexible targets using nextPYP.Nature protocols · 2026Review
- Structural Insights into Ordered Multicomponent Assemblies in Cell Junctions.Advances in experimental medicine and biology · 2026Review
- There and back again: a cell biologist's journey from organelles to molecules.Biological chemistry · 2025Review
- Automated removal of corrupted tilts in cryo-electron tomography.Journal of structural biology: X · 2025Article
- Strategies for studying discrete heterogeneity in situ using cryo-electron tomography.Current opinion in structural biology · 2025Review
- Distinct Target Site of Lenacapavir in Immature HIV-1 and Concurrent Binding with the Maturation Inhibitor Bevirimat.Journal of the American Chemical Society · 2025Article
- Cryo-EM single-particle analysis expanding towards increasingly native samples.Acta crystallographica. Section D, Structural biology · 2025Review
- Direct visualization of HIV-1 core nuclear import and its interplay with the nuclear pore.EMBO reports · 2025Article
- Advances in native cell membrane nanoparticles system.Current opinion in structural biology · 2025Review
- Structural basis for HIV-1 capsid adaption to a deficiency in IP6 packaging.Nature communications · 2025Article
- HIV-1 nuclear import is selective and depends on both capsid elasticity and nuclear pore adaptability.Nature microbiology · 2025Article
- Structural maturation of the matrix lattice is not required for HIV-1 particle infectivity.Science advances · 2025Article
- Rapid structural analysis of bacterial ribosomes in situ.Communications biology · 2025Article
- Leveraging Virtual Reality for Immersive Segmentation and Analysis of Cryo-Electron Tomography Data.Journal of visualized experiments : JoVE · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Cryo-electron tomography and subtomogram averaging (STA) has developed rapidly in recent years. It provides structures of macromolecular complexes in situ and in cellular context at or below subnanometer resolution and has led to unprecedented insights into the inner working of molecular machines in their native environment, as well as their functional relevant conformations and spatial distribution within biological cells or tissues. Given the tremendous potential of cryo-electron tomography STA in in situ structural cell biology, we previously developed emClarity, a graphics processing unit-accelerated image-processing software that offers STA and classification of macromolecular complexes at high resolution. However, the workflow remains challenging, especially for newcomers to the field. In this protocol, we describe a detailed workflow, processing and parameters associated with each step, from initial tomography tilt-series data to the final 3D density map, with several features unique to emClarity. We use four different samples, including human immunodeficiency virus type 1 Gag assemblies, ribosome and apoferritin, to illustrate the procedure and results of STA and classification. Following the processing steps described in this protocol, along with a comprehensive tutorial and guidelines for troubleshooting and parameter optimization, one can obtain density maps up to 2.8 Å resolution from six tilt series by cryo-electron tomography STA.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.