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- EMDB-39461: Cryo-EM structure of jasmonic acid transporter ABCG16 in digitonin -

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Basic information

Entry
Database: EMDB / ID: EMD-39461
TitleCryo-EM structure of jasmonic acid transporter ABCG16 in digitonin
Map data
Sample
  • Complex: Jasmonic acid transporter ABCG16
Keywordsjasmonate / transport / ABCG16 / JAT1 / cryo-EM / ABC transporter / plant hormone / MEMBRANE PROTEIN
Biological speciesArabidopsis (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsZhang X / Huang X / An N / Zhang P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Plants / Year: 2024
Title: Cryo-EM structure and molecular mechanism of the jasmonic acid transporter ABCG16.
Authors: Ning An / Xiaowei Huang / Zhao Yang / Minhua Zhang / Miaolian Ma / Fang Yu / Lianyan Jing / Boya Du / Yong-Fei Wang / Xue Zhang / Peng Zhang /
Abstract: Jasmonates (JAs) are a class of oxylipin phytohormones including jasmonic acid (JA) and derivatives that regulate plant growth, development and biotic and abiotic stress. A number of transporters ...Jasmonates (JAs) are a class of oxylipin phytohormones including jasmonic acid (JA) and derivatives that regulate plant growth, development and biotic and abiotic stress. A number of transporters have been identified to be responsible for the cellular and subcellular translocation of JAs. However, the mechanistic understanding of how these transporters specifically recognize and transport JAs is scarce. Here we determined the cryogenic electron microscopy structure of JA exporter AtABCG16 in inward-facing apo, JA-bound and occluded conformations, and outward-facing post translocation conformation. AtABCG16 structure forms a homodimer, and each monomer contains a nucleotide-binding domain, a transmembrane domain and an extracellular domain. Structural analyses together with biochemical and plant physiological experiments revealed the molecular mechanism by which AtABCG16 specifically recognizes and transports JA. Structural analyses also revealed that AtABCG16 features a unique bifurcated substrate translocation pathway, which is composed of two independent substrate entrances, two substrate-binding pockets and a shared apoplastic cavity. In addition, residue Phe608 from each monomer is disclosed to function as a gate along the translocation pathway controlling the accessing of substrate JA from the cytoplasm or apoplast. Based on the structural and biochemical analyses, a working model of AtABCG16-mediated JA transport is proposed, which diversifies the molecular mechanisms of ABC transporters.
History
DepositionMar 14, 2024-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39461.png

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Map

FileDownload / File: emd_39461.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 280 pix.
= 260.96 Å		0.93 Å/pix.
x 280 pix.
= 260.96 Å		0.93 Å/pix.
x 280 pix.
= 260.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
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Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-5.5751576 - 5.7695193
Average (Standard dev.)-0.00051129673 (±0.13125622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 260.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_39461_additional_1.map
Annotationunsharpened map
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Half map: #1

Fileemd_39461_half_map_1.map
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Half map: #2

Fileemd_39461_half_map_2.map
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Sample components

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Entire : Jasmonic acid transporter ABCG16

EntireName: Jasmonic acid transporter ABCG16
Components
  • Complex: Jasmonic acid transporter ABCG16

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Supramolecule #1: Jasmonic acid transporter ABCG16

SupramoleculeName: Jasmonic acid transporter ABCG16 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Arabidopsis (plant)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 237897
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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