Evidence map›Paper›PMID 28671674›Full record

ArticleNature methods2017

Addressing preferred specimen orientation in single-particle cryo-EM through tilting.

Yong Zi Tan, Philip R Baldwin, Joseph H Davis, James R Williamson, Clinton S Potter, Bridget Carragher, Dmitry Lyumkis

Abstract read
In one paragraph

Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 659 papers.

0numbers the graph read from it
0cells of the map it votes in
659citing 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

659 citing papers in PubMed.

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599 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

7 authors.

Yong Zi TanThe National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA.ORCID http://orcid.org/0000-0001-6656-6320
Philip R BaldwinThe National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA.ORCID http://orcid.org/0000-0002-4202-4129
Joseph H DavisDepartment of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.ORCID http://orcid.org/0000-0002-8858-8907
James R WilliamsonDepartment of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.ORCID http://orcid.org/0000-0002-8772-468X
Clinton S PotterThe National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA.ORCID http://orcid.org/0000-0002-3287-121X
Bridget CarragherThe National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA.ORCID http://orcid.org/0000-0002-0624-5020
Dmitry LyumkisLaboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, California, USA.ORCID http://orcid.org/0000-0002-8124-7472

Funding

X-ray Crystallographic Fragment Screening CoreU54AI150472 · NIAID · SEATTLE CHILDREN'S HOSPITAL · PI LYUMKIS, DMITRY · 2019 to 2021
$15.7M
TRD #3: An automated and streamlined pipeline for in-situ molecular microscopyP41GM103310 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI DE MARCO, ALEX, KIEFT, JEFFREY S · 2012 to 2021
$14.7M
TRAINING IN CELLULAR, MOLECULAR AND BIOPHYSICAL STUDIEST32GM008224 · NIGMS · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI LIEM, RONALD K. · 1987 to 2021
$9.9M
Pilot and Feasibility Project ProgramP30GM103331 · NIGMS · MEDICAL UNIVERSITY OF SOUTH CAROLINA · PI WESTWATER, CAROLINE · 2012 to 2016
$5.2M
Assembly of E. coli ribosomes in vitro and in cellsR37GM053757 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI WILLIAMSON, JAMES R · 2008 to 2017
$5.1M
STRUCTURE AND ASSEMBLY OF 30 S CENTRAL DOMAIN RNPSR01GM053757 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI WILLIAMSON, JAMES R · 1996 to 2020
$5.0M
Breaking Barriers in Structural Biology: Novel CryoEM Methods and ApplicationsDP5OD021396 · OD · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI LYUMKIS, DMITRY · 2015 to 2019
$2.4M
Continued Development and Maintenance of Appion SoftwareR01GM099678 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI CARRAGHER, BRIDGET OLIVIA, POTTER, CLINTON S · 2012 to 2015
$1.4M
Quantitation and biochemical characterization of autophagy's role in agingR00AG050749 · NIA · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI DAVIS, JOSEPH HARRY · 2017 to 2019
$744k
Quantitation and biochemical characterization of autophagy's role in agingK99AG050749 · NIA · SCRIPPS RESEARCH INSTITUTE, THE · PI DAVIS, JOSEPH HARRY · 2015 to 2016
$257k
NIAID NIH HHS U54 AI150472NIA NIH HHS K99 AG050749NIA NIH HHS R00 AG050749NIGMS NIH HHS P30 GM103331NIGMS NIH HHS P41 GM103310NIGMS NIH HHS R01 GM053757NIGMS NIH HHS R01 GM099678NIGMS NIH HHS R37 GM053757NIGMS NIH HHS T32 GM008224NIH HHS DP5 OD021396
6 · The paper itself

Abstract

We present a strategy for tackling preferred specimen orientation in single-particle cryogenic electron microscopy by employing tilts during data collection. We also describe a tool to quantify the resulting directional resolution using 3D Fourier shell correlation volumes. We applied these methods to determine the structures at near-atomic resolution of the influenza hemagglutinin trimer, which adopts a highly preferred specimen orientation, and of ribosomal biogenesis intermediates, which adopt moderately preferred orientations.

Indexed as

AlgorithmsCryoelectron MicroscopyHemagglutinin Glycoproteins, Influenza VirusImage EnhancementImaging, Three-DimensionalMolecular ImagingReproducibility of ResultsSensitivity and SpecificitySpecimen HandlingHemagglutinin Glycoproteins, Influenza Virus

Identifiers

PMID28671674
PMCPMC5533649

What OpenQuestion holds

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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.