Evidence map›Paper›PMID 42028876›Full record

ReviewIUCrJ2026

Making sense of invisible densities in single-particle cryo-EM.

Xiaoxuan Lin, Yifan Cheng

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in IUCrJ, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

2 authors.

Xiaoxuan LinHoward Hughes Medical Institute, University of California San Francisco, San Francisco, California, USA.
Yifan ChengHoward Hughes Medical Institute, University of California San Francisco, San Francisco, California, USA.ORCID 0000-0001-9535-0369

Funding

Project 3U54AI170792 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Nevan J Krogan · 2022 to 2026
$35.7M
Structural mechanism of integrin-mediated TGF-b activationR01HL134183 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Yifan Cheng, Stephen L Nishimura · 2016 to 2026
$5.9M
Conformational regulation of TGF-β activation by integrin αvβ6R01HL165175 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Yifan Cheng, Stephen L Nishimura · 2023 to 2026
$3.2M
Advancing cryo-EM technology to address difficult biological questionsR35GM140847 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Yifan Cheng · 2021 to 2026
$2.1M
Acquisition of an electron microscope for high-resolution single particle cryo-EMS10OD021741 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2016 to 2016
$2.0M
Glacios™ Cryo Transmission Electron Microscope with 200 kV XFEG opticsS10OD026881 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2019 to 2019
$1.8M
Linux cluster for near atomic resolution single particle cryo-EMS10OD020054 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2015 to 2015
$456k
National Institutes of Health, National Center for Research Resources S100D020054National Institutes of Health, National Center for Research Resources S100D021741National Institutes of Health, National Center for Research Resources S100D025881National Institutes of Health, National Heart, Lung, and Blood Institute R01HL134183National Institutes of Health, National Heart, Lung, and Blood Institute R01HL165175National Institutes of Health, National Institute of Allergy and Infectious Diseases U54AI170792National Institutes of Health, National Institute of General Medical Sciences R35GM140847NHLBI NIH HHS R01 HL134183NHLBI NIH HHS R01 HL165175NIAID NIH HHS U54 AI170792NIGMS NIH HHS R35 GM140847NIH HHS S10 OD020054NIH HHS S10 OD021741NIH HHS S10 OD026881
6 · The paper itself

Abstract

In the era of single-particle cryogenic electron microscopy (cryo-EM) and AI-driven protein structure prediction, obtaining high-resolution protein structures, either experimentally or computationally, has become increasingly routine. Yet studying and understanding protein dynamics remains challenging. In single-particle cryo-EM, protein dynamics are most obviously manifested as poor local resolution or disappearing densities in specific regions of a reconstruction. No method is yet available to computationally generate conformational ensembles that fully deconvolute these experimental observations. When dynamics are key to understanding protein function, it is clear to us that introducing new experimental approaches is necessary to close this gap and make sense of invisible densities in single-particle cryo-EM.

Indexed as

Cryoelectron MicroscopyProteinsSingle Molecule ImagingModels, MolecularProtein ConformationProteinscryo-EMhydrogen–deuterium exchange mass spectrometryprotein dynamicsprotein structures

Identifiers

PMID42028876
PMCPMC13134491

What OpenQuestion holds

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LicenceCC BY
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.