Evidence map›Paper›PMID 38626766›Full record

ArticleStructure (London, England : 1993)2024

Molecular basis for pH sensing in the KDEL trafficking receptor.

Zhiyi Wu, Kathryn Smith, Andreas Gerondopoulos, Tomoaki Sobajima, Joanne L Parker, Francis A Barr, Simon Newstead, Philip C Biggin

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Structure (London, England : 1993), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.9field-weighted citation impact, top 29% 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

3 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Article
  3. 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

8 authors at 1 institution in 1 country.

Zhiyi WuStructural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
Kathryn SmithDepartment of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK.
Andreas GerondopoulosDepartment of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
Tomoaki SobajimaDepartment of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
Joanne L ParkerDepartment of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK.
Francis A BarrDepartment of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
Simon NewsteadDepartment of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK. Electronic address: simon.newstead@bioch.ox.ac.uk.
Philip C BigginStructural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK. Electronic address: philip.biggin@bioch.ox.ac.uk.
University of Oxford · GB

Funding

Wellcome Trust 219531
6 · The paper itself

Abstract

Trafficking receptors control protein localization through the recognition of specific signal sequences that specify unique cellular locations. Differences in luminal pH are important for the vectorial trafficking of cargo receptors. The KDEL receptor is responsible for maintaining the integrity of the ER by retrieving luminally localized folding chaperones in a pH-dependent mechanism. Structural studies have revealed the end states of KDEL receptor activation and the mechanism of selective cargo binding. However, precisely how the KDEL receptor responds to changes in luminal pH remains unclear. To explain the mechanism of pH sensing, we combine analysis of X-ray crystal structures of the KDEL receptor at neutral and acidic pH with advanced computational methods and cell-based assays. We show a critical role for ordered water molecules that allows us to infer a direct connection between protonation in different cellular compartments and the consequent changes in the affinity of the receptor for cargo.

Indexed as

Receptors, PeptideBinding SitesCrystallography, X-RayEndoplasmic ReticulumHumansHydrogen-Ion ConcentrationModels, MolecularProtein BindingProtein TransportKDEL receptorReceptors, Peptidecargocomputationalendoplasmic reticulumGolgigrand canonical Monte CarloQMsimulationX-ray crystallography

Identifiers

PMID38626766
PMCPMC7617889
OpenAlexW4394824003

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.