Evidence map›Paper›PMID 30138616›Full record

ArticleJournal of molecular biology2018

Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography.

Wei Dai, Muyuan Chen, Christopher Myers, Steven J Ludtke, B Montgomery Pettitt, Jonathan A King, Michael F Schmid, Wah Chiu

Open access · greenAbstract read
In one paragraph

Article in Journal of molecular biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.

0numbers the graph read from it
0cells of the map it votes in
42citing papers in PubMed
2.2field-weighted citation impact, top 11% of its field
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

42 citing papers in PubMed, 67 citations in OpenAlex.

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  6. [COResearch square · 2026
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  9. Atomic view of photosynthetic metabolite permeability pathways and confinement in synthetic carboxysome shells.Proceedings of the National Academy of Sciences of the United States of America · 2024
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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

8 authors at 6 institutions in 1 country.

Wei DaiDepartment of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA. Electronic address: wd157@dls.rutgers.edu.
Muyuan ChenVerna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
Christopher MyersDepartment of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
Steven J LudtkeVerna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
B Montgomery PettittDepartment of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA.
Jonathan A KingDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Michael F SchmidDivision of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA.
Wah ChiuDivision of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA; Departments of Bioengineering and of Microbiology and Immunoplogy, James H. Clark Center, Stanford University, Stanford, CA 94305, USA. Electronic address: wahc@stanford.edu.
Baylor College of Medicine · USThe University of Texas Medical Branch at Galveston · USMassachusetts Institute of Technology · USRutgers, The State University of New Jersey · USSLAC National Accelerator Laboratory · USStanford University · US

Funding

3 D ELECTRON MICROSCOPY OF MACROMOLECULES (5P41RR002250-27)P41GM103832 · NIGMS · STANFORD UNIVERSITY · PI CHIU, WAH · 2012 to 2019
$15.1M
Theory of Proteins and Peptides in SolutionR01GM037657 · NIGMS · UNIVERSITY OF TEXAS MED BR GALVESTON · PI PETTITT, BERNARD MONTGOMERY · 1988 to 2023
$5.5M
SUPPORT AND DEVELOPMENT OF EMAN FOR ELECTRON MICROSCOPY IMAGE PROCESSINGR01GM080139 · NIGMS · BAYLOR COLLEGE OF MEDICINE · PI LUDTKE, STEVEN J · 2006 to 2022
$5.4M
NIGMS NIH HHS P41 GM103832NIGMS NIH HHS R01 GM037657NIGMS NIH HHS R01 GM080139
6 · The paper itself

Abstract

Cyanobacteria are photosynthetic organisms responsible for ~25% of the organic carbon fixation on earth. A key step in carbon fixation is catalyzed by ribulose bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme in the biosphere. Applying Zernike phase-contrast electron cryo-tomography and automated annotation, we identified individual RuBisCO molecules and their assembly intermediates leading to the formation of carboxysomes inside Syn5 cyanophage infected cyanobacteria Synechococcus sp. WH8109 cells. Surprisingly, more RuBisCO molecules were found to be present as cytosolic free-standing complexes or clusters than as packaged assemblies inside carboxysomes. Cytosolic RuBisCO clusters and partially assembled carboxysomes identified in the cell tomograms support a concurrent assembly model involving both the protein shell and the enclosed RuBisCO. In mature carboxysomes, RuBisCO is neither randomly nor strictly icosahedrally packed within protein shells of variable sizes. A time-averaged molecular dynamics simulation showed a semi-liquid probability distribution of the RuBisCO in carboxysomes and correlated well with carboxysome subtomogram averages. Our structural observations reveal the various stages of RuBisCO assemblies, which could be important for understanding cellular function.

Indexed as

Cryoelectron MicroscopyAnimalsAquatic OrganismsCyanobacteriaMiceMolecular ConformationMolecular Dynamics SimulationRibulose-Bisphosphate CarboxylaseRibulose-Bisphosphate Carboxylasecarboxysome biogenesisconvolutional neural network-based annotationmolecular dynamics simulationRuBisCOzernike phase-contrast cryo-electron tomography

Identifiers

PMID30138616
PMCPMC6252266
OpenAlexW2888697479

What OpenQuestion holds

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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.