Evidence map›Paper›PMID 29809143›Full record

ArticleeLife2018

Routine single particle CryoEM sample and grid characterization by tomography.

Alex J Noble, Venkata P Dandey, Hui Wei, Julia Brasch, Jillian Chase, Priyamvada Acharya, Yong Zi Tan, Zhening Zhang, Laura Y Kim, Giovanna Scapin and 11 more

Open access · goldAbstract read
In one paragraph

Article in eLife, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 179 papers.

0numbers the graph read from it
0cells of the map it votes in
179citing papers in PubMed
28.7field-weighted citation impact, top 1% 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

179 citing papers in PubMed, 308 citations in OpenAlex.

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119 more citing papers are in PubMed but not listed here.

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

21 authors at 5 institutions in 1 country.

Alex J NobleNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.ORCID http://orcid.org/0000-0001-8634-2279
Venkata P Dandey *National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.
Hui Wei *National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.
Julia BraschNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.
Jillian ChaseDepartment of Chemistry and Biochemistry, City College of New York, New York, United States.
Priyamvada AcharyaNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.
Yong Zi TanNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.ORCID http://orcid.org/0000-0001-6656-6320
Zhening ZhangNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.
Laura Y KimNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.
Giovanna ScapinNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.
Micah RappNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.
Edward T EngNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.ORCID http://orcid.org/0000-0002-8014-7269
William J RiceNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.
Anchi ChengNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.
Carl J NegroNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.
Lawrence ShapiroDepartment of Biochemistry and Molecular Biophysics, Columbia University, New York, United States.
Peter D KwongVaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Maryland, United States.
David JeruzalmiDepartment of Chemistry and Biochemistry, City College of New York, New York, United States.ORCID http://orcid.org/0000-0001-5886-1370
Amedee des GeorgesDepartment of Chemistry and Biochemistry, City College of New York, New York, United States.
Clinton S PotterNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.ORCID http://orcid.org/0000-0003-2394-0831
Bridget CarragherNational Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.ORCID http://orcid.org/0000-0002-0624-5020
New York Structural Biology Center · USThe Graduate Center, CUNY · USNational Institutes of Health · USColumbia University · USMerck & Co., Inc., Rahway, NJ, USA (United States) · US

Funding

TRD #3: An automated and streamlined pipeline for in-situ molecular microscopyP41GM103310 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI KIEFT, JEFFREY S · 2012 to 2021
$14.7M
Cellular/Molecular Basis of Development: Research CenterG12MD007603 · NIMHD · CITY COLLEGE OF NEW YORK · PI PEZZANO, MARK · 2012 to 2017
$11.5M
Replication Initiation in Bacteria and EukaryotesR01GM084162 · NIGMS · HARVARD UNIVERSITY · PI JERUZALMI, DAVID · 2009 to 2012
$1.5M
Acquisition of Detector for JEOL 3200 FSC Electron MicroscopeS10OD019994 · OD · NEW YORK STRUCTURAL BIOLOGY CENTER · PI CARRAGHER, BRIDGET OLIVIA · 2015 to 2015
$600k
NIAID NIH HHS Intramural Funding from the Vaccine Research CenterNIGMS NIH HHS GM103310NIGMS NIH HHS P41 GM103310NIGMS NIH HHS R01 GM084162NIH HHS R01 GM084162NIH HHS R01-MH1148175NIH HHS S10 OD019994NIH HHS S10 OD019994-01NIMHD NIH HHS 5G12MD007603-30NIMHD NIH HHS G12 MD007603
6 · The paper itself

Abstract

Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment.

Indexed as

AirAnimalsApoferritinsCryoelectron MicroscopyDnaB HelicasesElectron Microscope TomographyEscherichia coliFructose-Bisphosphate AldolaseProteasome Endopeptidase ComplexRabbitsSugar Alcohol DehydrogenasesSurface PropertiesWaterApoferritinsDnaB HelicasesdnaB protein, E coliFructose-Bisphosphate Aldolasegalactitol 2-dehydrogenaseProteasome Endopeptidase ComplexSugar Alcohol DehydrogenasesWaterair-watercryoETfiducial-lessmolecular biophysicsnoneprotomosingle particlestructural biologytomography

Identifiers

PMID29809143
PMCPMC5999397
OpenAlexW2949882099

What OpenQuestion holds

Textmetadata
LicenceCC0
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.