Evidence map›Paper›PMID 36424382›Full record

ArticleNature communications2022

Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter.

Atsushi Yamagata, Yoshiko Murata, Kosuke Namba, Tohru Terada, Shuya Fukai, Mikako Shirouzu

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
6.1field-weighted citation impact, top 4% 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

14 citing papers in PubMed, 36 citations in OpenAlex.

  1. Review
  2. Article
  3. Review
  4. Conformational Dynamics of NaJournal of chemical information and modeling · 2026
    Article
  5. Article
  6. Article
  7. ZmPRR37-ZmYSL14 module enhances salt stress tolerance in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025
    Article
  8. Article
  9. Review
  10. Review
  11. Article
  12. Article
  13. Review
  14. Iron sensing in plants.Frontiers in plant science · 2023
    Review
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

6 authors at 5 institutions in 1 country.

Atsushi YamagataLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan. atsushi.yamagata@riken.jp.ORCID 0000-0001-9285-1256
Yoshiko MurataBioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, Japan.ORCID 0000-0003-1891-2609
Kosuke NambaDepartment of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shoumachi, Tokushima-shi, Tokushima, Japan.ORCID 0000-0003-1548-5656
Tohru TeradaDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.ORCID 0000-0002-7091-0646
Shuya FukaiDepartment of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, Japan.ORCID 0000-0002-1241-1443
Mikako ShirouzuLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.ORCID 0000-0002-7997-2149
RIKEN Center for Biosystems Dynamics Research · JPKyoto University · JPSuntory Foundation for Life Sciences · JPThe University of Tokyo · JPTokushima University · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Calcareous soils cover one-third of all land and cause severe growth defects in plants due to the poor water solubility of iron at high pH. Poaceae species use a unique chelation strategy, whereby plants secrete a high-affinity metal chelator, known as phytosiderophores (mugineic acids), and reabsorb the iron-phytosiderophore complex by the yellow stripe 1/yellow stripe 1-like (YS1/YSL) transporter for efficient uptake of iron from the soil. Here, we present three cryo-electron microscopy structures of barley YS1 (HvYS1) in the apo state, in complex with an iron-phytosiderophore complex, Fe(III)-deoxymugineic acid (Fe(III)-DMA), and in complex with the iron-bound synthetic DMA analog (Fe(III)-PDMA). The structures reveal a homodimeric assembly mediated through an anti-parallel β-sheet interaction with cholesterol hemisuccinate. Each protomer adopts an outward open conformation, and Fe(III)-DMA is bound near the extracellular space in the central cavity. Fe(III)-PDMA occupies the same binding site as Fe(III)-DMA, demonstrating that PDMA can function as a potent fertilizer in an essentially identical manner to DMA. Our results provide a structural framework for iron-phytosiderophore recognition and transport by YS1/YSL transporters, which will enable the rational design of new, high-potency fertilizers.

Indexed as

IronSoilCryoelectron MicroscopyMembrane Transport ProteinsPlant ProteinsPlantsZea maysIronMembrane Transport ProteinsPlant ProteinsSoil

Identifiers

PMID36424382
PMCPMC9691689
OpenAlexW4310060719

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.