Evidence map›Paper›PMID 35136165›Full record

ArticleCommunications biology2022

An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking.

Debajit Dey, Suruchi Singh, Saif Khan, Matthew Martin, Nicholas J Schnicker, Lokesh Gakhar, Brian G Pierce, S Saif Hasan

Open access · goldAbstract read
In one paragraph

Article in Communications biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
2.2field-weighted citation impact, top 11% 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

16 citing papers in PubMed, 25 citations in OpenAlex.

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  15. Retro-2 alters Golgi structure.Scientific reports · 2022
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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

8 authors at 4 institutions in 1 country.

Debajit Dey *Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-8289-7904
Suruchi Singh *Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
Saif KhanProtein and Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.ORCID http://orcid.org/0000-0002-3604-2670
Matthew MartinDepartment of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
Nicholas J SchnickerProtein and Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.ORCID http://orcid.org/0000-0002-5189-4943
Lokesh GakharProtein and Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
Brian G PierceW.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.ORCID http://orcid.org/0000-0003-4821-0368
S Saif HasanDepartment of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA. sshasan@som.umaryland.edu.ORCID http://orcid.org/0000-0002-0759-7511
University of Maryland, Baltimore · USUniversity of Iowa · USAdvanced Bioscience Laboratories (United States) · USUniversity of Southern California · US

Funding

Viral VectorP30CA086862 · NCI · UNIVERSITY OF IOWA · PI Christopher K Laubenthal · 2000 to 2026
$70.0M
UNIVERSITY OF MARYLAND GREENEBAUM CANCER CENTERSUPPORT GRANTP30CA134274 · NCI · UNIVERSITY OF MARYLAND BALTIMORE · PI Vu H. Duong · 2008 to 2026
$51.0M
User Training & OutreachP30GM138396 · NIGMS · UCHICAGO ARGONNE, LLC · PI JANET L. SMITH · 2020 to 2026
$34.3M
The Midwest Center for Structural Genomics - Community ResourceR24GM115586 · NIGMS · UNIVERSITY OF CHICAGO · PI JOACHIMIAK, ANDRZEJ · 2015 to 2017
$2.8M
NCI NIH HHS P30 CA086862NCI NIH HHS P30 CA134274NIGMS NIH HHS P30 GM138396NIGMS NIH HHS R24 GM115586
6 · The paper itself

Abstract

β-Coronaviruses such as SARS-CoV-2 hijack coatomer protein-I (COPI) for spike protein retrograde trafficking to the progeny assembly site in endoplasmic reticulum-Golgi intermediate compartment (ERGIC). However, limited residue-level details are available into how the spike interacts with COPI. Here we identify an extended COPI binding motif in the spike that encompasses the canonical K-x-H dibasic sequence. This motif demonstrates selectivity for αCOPI subunit. Guided by an in silico analysis of dibasic motifs in the human proteome, we employ mutagenesis and binding assays to show that the spike motif terminal residues are critical modulators of complex dissociation, which is essential for spike release in ERGIC. αCOPI residues critical for spike motif binding are elucidated by mutagenesis and crystallography and found to be conserved in the zoonotic reservoirs, bats, pangolins, camels, and in humans. Collectively, our investigation on the spike motif identifies key COPI binding determinants with implications for retrograde trafficking.

Indexed as

Amino Acid MotifsAmino Acid SequenceBinding SitesCoatomer ProteinCoat Protein Complex IComputer SimulationCOVID-19Endoplasmic ReticulumGolgi ApparatusHEK293 CellsHumansModels, MolecularMutationPhylogenyProtein BindingProtein DomainsCoatomer ProteinCoat Protein Complex ISpike Glycoprotein, Coronavirusspike protein, SARS-CoV-2

Identifiers

PMID35136165
PMCPMC8825798
OpenAlexW4210917601

What OpenQuestion holds

Textmetadata
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.