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Yorodumi- PDB-7wst: Cryo-EM structure of the barley Yellow stripe 1 transporter in co... -
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-Basic information
Entry | Database: PDB / ID: 7wst | ||||||
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Title | Cryo-EM structure of the barley Yellow stripe 1 transporter in complex with Fe(III)-DMA | ||||||
Components | Iron-phytosiderophore transporter | ||||||
Keywords | METAL TRANSPORT / iron-phytosiderophore transporter / deoxymugineic acid | ||||||
Function / homology | Function and homology information oligopeptide transmembrane transporter activity / iron-nicotianamine transmembrane transporter activity / seed development / response to iron ion / plasma membrane Similarity search - Function | ||||||
Biological species | Hordeum vulgare (barley) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Yamagata, A. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Uptake mechanism of iron-phytosiderophore from the soil based on the structure of yellow stripe transporter. Authors: Atsushi Yamagata / Yoshiko Murata / Kosuke Namba / Tohru Terada / Shuya Fukai / Mikako Shirouzu / 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 ...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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wst.cif.gz | 216.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wst.ent.gz | 172.1 KB | Display | PDB format |
PDBx/mmJSON format | 7wst.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wst_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7wst_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7wst_validation.xml.gz | 53.5 KB | Display | |
Data in CIF | 7wst_validation.cif.gz | 76.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/7wst ftp://data.pdbj.org/pub/pdb/validation_reports/ws/7wst | HTTPS FTP |
-Related structure data
Related structure data | 32766MC 7wsrC 7wsuC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 76070.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) / Gene: HvYS1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q2PGC4 #2: Chemical | ChemComp-Y01 / #3: Chemical | #4: Chemical | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Yellow stripe 1 in the apo state / Type: CELL / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Hordeum vulgare (barley) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 471603 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.19 Å2 | ||||||||||||||||||||||||
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