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- 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
TitleCryo-EM structure of the barley Yellow stripe 1 transporter in complex with Fe(III)-DMA
ComponentsIron-phytosiderophore transporter
KeywordsMETAL TRANSPORT / iron-phytosiderophore transporter / deoxymugineic acid
Function / homologyMetal-nicotianamine transporter YSL-like / Oligopeptide transporter, OPT superfamily / OPT oligopeptide transporter protein / oligopeptide transmembrane transporter activity / plasma membrane / Chem-554 / : / CHOLESTEROL HEMISUCCINATE / Iron-phytosiderophore transporter
Function and homology information
Biological speciesHordeum vulgare (barley)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsYamagata, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: 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
DepositionFeb 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-phytosiderophore transporter
B: Iron-phytosiderophore transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,80910
Polymers152,1422
Non-polymers2,6678
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Iron-phytosiderophore transporter


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 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H50O4
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-554 / (2~{S})-1-[(3~{S})-3-[[(3~{S})-3,4-bis(oxidanyl)-4-oxidanylidene-butyl]amino]-4-oxidanyl-4-oxidanylidene-butyl]azetidine-2-carboxylic acid


Mass: 304.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N2O7
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Yellow stripe 1 in the apo state / Type: CELL / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Hordeum vulgare (barley)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
9RELION3.1initial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 471603 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 45.19 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039716
ELECTRON MICROSCOPYf_angle_d0.551613224
ELECTRON MICROSCOPYf_chiral_restr0.03861494
ELECTRON MICROSCOPYf_plane_restr0.00421590
ELECTRON MICROSCOPYf_dihedral_angle_d5.77841338

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