Evidence map›Paper›PMID 36842118›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

In Situ Structure Determination of Bacterial Surface Nanomachines Using Cryo-Electron Tomography.

Longsheng Lai, Yee-Wai Cheung, Matthew Martinez, Kathryn Kixmoeller, Leon Palao, Stefan Steimle, Meng-Chiao Ho, Ben E Black, Erh-Min Lai, Yi-Wei Chang

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Longsheng LaiDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Yee-Wai CheungDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Matthew MartinezDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Kathryn KixmoellerDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Leon PalaoDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Stefan SteimleDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Meng-Chiao HoInstitute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
Ben E BlackDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Erh-Min LaiInstitute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.
Yi-Wei ChangDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. ywc@pennmedicine.upenn.edu.

Funding

Centromere identity, strength, and regulationR35GM130302 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI Ben E. Black · 2019 to 2026
$4.3M
Novel machine learning approaches for improving structural discrimination in cryo-electron tomography-Administrative SupplementR01GM134020 · NIGMS · CARNEGIE-MELLON UNIVERSITY · PI XU, MIN · 2020 to 2023
$1.4M
Investigating the structure and function of the human centromere and kinetochoreF30CA261198 · NCI · UNIVERSITY OF PENNSYLVANIA · PI KIXMOELLER, KATHRYN · 2021 to 2024
$163k
NIGMS NIH HHS R01 GM134020NIGMS NIH HHS R35 GM130302
6 · The paper itself

Abstract

Bacterial surface nanomachines are often refractory to structural determination in their intact form due to their extensive association with the cell envelope preventing them from being properly purified for traditional structural biology methods. Cryo-electron tomography (cryo-ET) is an emerging branch of cryo-electron microscopy that can visualize supramolecular complexes directly inside frozen-hydrated cells in 3D at nanometer resolution, therefore posing a unique capability to study the intact structures of bacterial surface nanomachines in situ and reveal their molecular association with other cellular components. Furthermore, the resolution of cryo-ET is continually improving alongside methodological advancement. Here, using the type IV pilus machine in Myxococcus xanthus as an example, we describe a step-by-step workflow for in situ structure determination including sample preparation and screening, microscope and camera tuning, tilt series acquisition, data processing and tomogram reconstruction, subtomogram averaging, and structural analysis.

Indexed as

Electron Microscope TomographyImage Processing, Computer-AssistedCryoelectron MicroscopyWorkflowBacterial nanomachinesCryo-electron tomographyCryo-ET grid screeningDynamoElectron microscope alignmentIMODIn situ structural biologySerialEMSubtomogram averagingTilt series acquisition

Identifiers

PMID36842118

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.