Evidence map›Paper›PMID 35194584›Full record

ArticleSTAR protocols2022

Protocol for structure determination of SARS-CoV-2 main protease at near-physiological-temperature by serial femtosecond crystallography.

Fatma Betul Ertem, Omur Guven, Cengizhan Buyukdag, Oktay Gocenler, Esra Ayan, Busra Yuksel, Mehmet Gul, Gozde Usta, Barıs Cakılkaya, J Austin Johnson and 14 more

Abstract read
In one paragraph

Article in STAR protocols, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing 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

10 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. Article
  8. Review
  9. Article
  10. Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source "Turkish journal of biology = Turk biyoloji dergisi · 2023
    Article
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

24 authors.

Fatma Betul ErtemDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
Omur GuvenDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
Cengizhan BuyukdagDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
Oktay GocenlerDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
Esra AyanDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
Busra YukselDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
Mehmet GulDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
Gozde UstaDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
Barıs CakılkayaDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
J Austin JohnsonDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
E Han DaoLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA.
Zhen SuLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA.
Frederic PoitevinLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA.
Chun Hong YoonLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA.
Christopher KupitzLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA.
Brandon HayesLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA.
Mengning LiangLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA.
Mark S HunterLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA.
Alexander BatyukLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA.
Raymond G SierraLinac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, 94025 CA, USA.
Gihan KetawalaDepartment of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
Sabine BothaDepartment of Physics, Arizona State University, Tempe, AZ 85287-1504, USA.
Çağdaş DağDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.
Hasan DeMirciDepartment of Molecular Biology and Genetics, Koc University, Istanbul, Turkey.

Funding

X-ray Absorption Spectroscopy (XAS) pp.711-759P41GM103393 · NIGMS · STANFORD UNIVERSITY · PI HODGSON, KEITH O · 2012 to 2019
$30.6M
NIGMS NIH HHS P41 GM103393
6 · The paper itself

Abstract

The SARS-CoV-2 main protease of (Mpro) is an important target for SARS-CoV-2 related drug repurposing and development studies. Here, we describe the steps for structural characterization of SARS-CoV-2 Mpro, starting from plasmid preparation and protein purification. We detail the steps for crystallization using the sitting drop, microbatch (under oil) approach. Finally, we cover data collection and structure determination using serial femtosecond crystallography. For complete details on the use and execution of this protocol, please refer to Durdagi et al. (2021).

Indexed as

Models, MolecularCoronavirus 3C ProteasesCrystallizationCrystallography, X-RayHumansSARS-CoV-23C-like proteinase, SARS-CoV-2Coronavirus 3C ProteasesProtein BiochemistryProtein expression and purificationStructural BiologyX-ray Crystallography

Identifiers

PMID35194584
PMCPMC8784426

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.