Evidence map›Paper›PMID 37546986›Full record

ArticlebioRxiv : the preprint server for biology2023

Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking.

Un Seng Chio, Eugene Palovcak, Anton A A Autzen, Henriette E Autzen, Elise N Muñoz, Zanlin Yu, Feng Wang, David A Agard, Jean-Paul Armache, Geeta J Narlikar and 1 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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, 4 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors at 5 institutions in 2 countries.

Un Seng ChioDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Eugene PalovcakBiophysics Graduate Program, University of California San Francisco, San Francisco, CA, USA.
Anton A A AutzenDepartment of Materials Science & Engineering, Stanford University, Stanford, CA, USA.
Henriette E AutzenDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Elise N MuñozTetrad Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
Zanlin YuDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Feng WangDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
David A AgardDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Jean-Paul ArmacheDepartment of Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
Geeta J NarlikarDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
Yifan ChengDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
University of California, San Francisco · USHoward Hughes Medical Institute · USPennsylvania State University · USTechnical University of Denmark · DKUniversity of Copenhagen · DK

Funding

STRUCTURAL BIOLOGY TRAINING PROGRAMT32GM008284 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 1988 to 2022
$10.1M
Measuring the lifetime and mechanical stability of phase-separated heterochromatin domainsR35GM127020 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI GEETA J NARLIKAR · 2018 to 2026
$7.3M
ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale ModelingR01GM129325 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERRIN, THOMAS E · 2018 to 2025
$5.2M
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
Linux cluster for near atomic resolution single particle cryo-EMS10OD020054 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHENG, YIFAN · 2015 to 2015
$456k
Molecular mechanisms of the ACF chromatin remodeling complexF32GM137463 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHIO, UN SENG · 2020 to 2022
$201k
NIGMS NIH HHS F32 GM137463NIGMS NIH HHS R01 GM129325NIGMS NIH HHS R35 GM127020NIGMS NIH HHS R35 GM140847NIGMS NIH HHS T32 GM008284NIH HHS S10 OD020054NIH HHS S10 OD021741
6 · The paper itself

Abstract

Single-particle cryo-EM is widely used to determine enzyme-nucleosome complex structures. However, cryo-EM sample preparation remains challenging and inconsistent due to complex denaturation at the air-water interface (AWI). To address this issue, we developed graphene-oxide-coated EM grids functionalized with either single-stranded DNA (ssDNA) or thiol-poly(acrylic acid-co-styrene) (TAASTY) co-polymer. These grids protect complexes between the chromatin remodeler SNF2h and nucleosomes from the AWI and facilitated collection of high-quality micrographs of intact SNF2h-nucleosome complexes in the absence of crosslinking. The data yields maps ranging from 2.3 to 3 Å in resolution. 3D variability analysis reveals nucleotide-state linked conformational changes in SNF2h bound to a nucleosome. In addition, the analysis provides structural evidence for asymmetric coordination between two SNF2h protomers acting on the same nucleosome. We envision these grids will enable similar detailed structural analyses for other enzyme-nucleosome complexes and possibly other protein-nucleic acid complexes in general.

Indexed as

chromatin remodelergraphene oxideISWInucleosomesingle-particle cryo-EMSNF2h

Identifiers

PMID37546986
PMCPMC10402172
OpenAlexW4381513019

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.