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- PDB-7wsr: Cryo-EM structure of the barley Yellow stripe 1 transporter -

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Basic information

Entry
Database: PDB / ID: 7wsr
TitleCryo-EM structure of the barley Yellow stripe 1 transporter
ComponentsIron-phytosiderophore transporter
KeywordsMETAL TRANSPORT / iron-phytosiderophore transporter
Function / homology
Function and homology information


iron-nicotianamine transmembrane transporter activity / oligopeptide transmembrane transporter activity / seed development / response to iron ion / plasma membrane
Similarity search - Function
Oligopeptide transporter, OPT superfamily / Metal-nicotianamine transporter YSL-like / OPT oligopeptide transporter protein
Similarity search - Domain/homology
CHOLESTEROL HEMISUCCINATE / Iron-phytosiderophore transporter
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 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 18, 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
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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)154,0896
Polymers152,1422
Non-polymers1,9474
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNALAA1 - 600
d_12ens_1Y01Y01B
d_13ens_1Y01Y01C
d_21ens_1GLNALAD1 - 600
d_22ens_1Y01Y01E
d_23ens_1Y01Y01F

NCS oper: (Code: given
Matrix: (-1, 1.36683492964E-7, -2.42880329946E-8), (-1.36683492679E-7, -1, -1.17547299347E-8), (-2.42880346013E-8, -1.17547266149E-8, 1)
Vector: 331.399984573, 331.400023942, 5.91576286979E-6)

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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 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 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
7Cootmodel fitting
9RELION3.1.3initial Euler assignment
10RELION3.1.3final Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 319121 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 52.92 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00239642
ELECTRON MICROSCOPYf_angle_d0.411113122
ELECTRON MICROSCOPYf_chiral_restr0.0361486
ELECTRON MICROSCOPYf_plane_restr0.00341580
ELECTRON MICROSCOPYf_dihedral_angle_d9.63283336
Refine LS restraints NCSType: NCS constraints / Rms dev position: 7.28967564945E-5 Å

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