Evidence map›Paper›PMID 34062386›Full record

ArticleUltramicroscopy2021

Gold nanoparticles and tilt pairs to assess protein flexibility by cryo-electron microscopy.

Milind Jagota, Raphael J L Townshend, Lin-Woo Kang, David A Bushnell, Ron O Dror, Roger D Kornberg, Maia Azubel

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Ultramicroscopy, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

7 authors.

Milind JagotaDepartment of Computer Science, Stanford University, Stanford, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA.
Raphael J L TownshendDepartment of Computer Science, Stanford University, Stanford, CA, USA.
Lin-Woo KangDepartment of Biological Sciences, Konkuk University, Seoul, Korea.
David A BushnellDepartment of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Ron O DrorDepartment of Computer Science, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
Roger D KornbergDepartment of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Maia AzubelDepartment of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. Electronic address: mazubel@stanford.edu.

Funding

Structure of the Eukaryote Transcription ApparatusR01AI021144 · NIAID · STANFORD UNIVERSITY · PI KORNBERG, ROGER D · 1985 to 2018
$10.3M
Three-Dimensional Structure of Eukaryote ChromosomesR01DK121366 · NIDDK · STANFORD UNIVERSITY · PI LEVITT, MICHAEL · 2018 to 2021
$4.8M
NIAID NIH HHS R01 AI021144NIDDK NIH HHS R01 DK121366
6 · The paper itself

Abstract

A computational method was developed to recover the three-dimensional coordinates of gold nanoparticles specifically attached to a protein complex from tilt-pair images collected by electron microscopy. The program was tested on a simulated dataset and applied to a real dataset comprising tilt-pair images recorded by cryo electron microscopy of RNA polymerase II in a complex with four gold-labeled single-chain antibody fragments. The positions of the gold nanoparticles were determined, and comparison of the coordinates among the tetrameric particles revealed the range of motion within the protein complexes.

Indexed as

Immunoglobulin FragmentsRNA Polymerase IICryoelectron MicroscopyGoldImage Processing, Computer-AssistedMetal NanoparticlesModels, MolecularProtein BindingGoldImmunoglobulin FragmentsRNA Polymerase IICryo-electron microscopyGold nanoparticlesLeast-squares methodSingle-chain Fv antibodyTilt-pairs

Identifiers

PMID34062386
PMCPMC8238918

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.