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- EMDB-37840: Cryo-EM structure of AtABCG16 -

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Basic information

Entry
Database: EMDB / ID: EMD-37840
TitleCryo-EM structure of AtABCG16
Map data
Sample
  • Complex: Homodimer of ABCG16
    • Protein or peptide: AtABCG16
Keywordsjasmonate / transport / cryo-EM / ABC transporter / plant hormone / MEMBRANE PROTEIN
Function / homology
Function and homology information


pollen wall assembly / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
: / ABC-2 type transporter / ABC-2 type transporter / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter G family member 16
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsHuang X / An N / Zhang X / 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
DepositionOct 19, 2023-
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_37840.png

Downloads & links

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Map

FileDownload / File: emd_37840.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.5669541 - 3.6546574
Average (Standard dev.)-0.0044543087 (±0.076473504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_37840_additional_1.map
Annotationunsharpened map
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Half map: #1

Fileemd_37840_half_map_1.map
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Half map: #2

Fileemd_37840_half_map_2.map
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Sample components

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Entire : Homodimer of ABCG16

EntireName: Homodimer of ABCG16
Components
  • Complex: Homodimer of ABCG16
    • Protein or peptide: AtABCG16

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Supramolecule #1: Homodimer of ABCG16

SupramoleculeName: Homodimer of ABCG16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: AtABCG16

MacromoleculeName: AtABCG16 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSRILVEDDN ATPFHSMEII SSSLTLGQLL KNVSDVRKVE VGDETPVHEF FDRDGSSLDG DNDHLMRPV PFVLSFNNLT YNVSVRRKLD FHDLVPWRRT SFSKTKTLLD NISGETRDGE I LAVLGASG SGKSTLIDAL ANRIAKGSLK GTVTLNGEAL QSRMLKVISA ...String:
MSRILVEDDN ATPFHSMEII SSSLTLGQLL KNVSDVRKVE VGDETPVHEF FDRDGSSLDG DNDHLMRPV PFVLSFNNLT YNVSVRRKLD FHDLVPWRRT SFSKTKTLLD NISGETRDGE I LAVLGASG SGKSTLIDAL ANRIAKGSLK GTVTLNGEAL QSRMLKVISA YVMQDDLLFP ML TVEETLM FAAEFRLPRS LPKSKKKLRV QALIDQLGIR NAAKTIIGDE GHRGISGGER RRV SIGIDI IHDPIVLFLD EPTSGLDSTS AFMVVKVLKR IAESGSIIIM SIHQPSHRVL SLLD RLIFL SRGHTVFSGS PASLPSFFAG FGNPIPENEN QTEFALDLIR ELEGSAGGTR GLVEF NKKW QEMKKQSNPQ TLTPPASPNP NLTLKEAISA SISRGKLVSG GGGGSSVINH GGGTLA VPA FANPFWIEIK TLTRRSILNS RRQPELLGMR LATVIVTGFI LATVFWRLDN SPKGVQE RL GFFAFAMSTM FYTCADALPV FLQERYIFMR ETAYNAYRRS SYVLSHAIVT FPSLIFLS L AFAVTTFWAV GLEGGLMGFL FYCLIILASF WSGSSFVTFL SGVVPHVMLG YTIVVAILA YFLLFSGFFI NRDRIPQYWI WFHYLSLVKY PYEAVLQNEF SDPTECFVRG VQLFDNSPLG ELTYGMKLR LLDSVSRSIG MRISSSTCLT TGADVLKQQG VTQLSKWNCL LITVGFGFLF R ILFYLCLL LGSKNKRR

UniProtKB: ABC transporter G family member 16

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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 179411
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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