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- EMDB-35146: Cryo-EM structure of abscisic acid transporter AtABCG25 with ABA -

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Basic information

Entry
Database: EMDB / ID: EMD-35146
TitleCryo-EM structure of abscisic acid transporter AtABCG25 with ABA
Map data
Sample
  • Complex: Arabidopsis thaliana ABCG25
    • Protein or peptide: ABC transporter G family member 25
  • Ligand: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
Keywordsabscisic acid / transport / ABC transporter / plant hormone / MEMBRANE PROTEIN
Function / homologyProtein of unknown function DUF1425 / YcfL-like superfamily / Protein of unknown function (DUF1425) / Prokaryotic membrane lipoprotein lipid attachment site profile. / DUF1425 domain-containing protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsHuang X / Zhang X / Zhang P
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Plants / Year: 2023
Title: Cryo-EM structure and molecular mechanism of abscisic acid transporter ABCG25.
Authors: Xiaowei Huang / Xue Zhang / Ning An / Minhua Zhang / Miaolian Ma / Yang Yang / Lianyan Jing / Yongfei Wang / Zhenguo Chen / Peng Zhang /
Abstract: Abscisic acid (ABA) is one of the plant hormones that regulate various physiological processes, including stomatal closure, seed germination and development. ABA is synthesized mainly in vascular ...Abscisic acid (ABA) is one of the plant hormones that regulate various physiological processes, including stomatal closure, seed germination and development. ABA is synthesized mainly in vascular tissues and transported to distal sites to exert its physiological functions. Many ABA transporters have been identified, however, the molecular mechanism of ABA transport remains elusive. Here we report the cryogenic electron microscopy structure of the Arabidopsis thaliana adenosine triphosphate-binding cassette G subfamily ABA exporter ABCG25 (AtABCG25) in inward-facing apo conformation, ABA-bound pre-translocation conformation and outward-facing occluded conformation. Structural and biochemical analyses reveal that the ABA bound with ABCG25 adopts a similar configuration as that in ABA receptors and that the ABA-specific binding is dictated by residues from transmembrane helices TM1, TM2 and TM5a of each protomer at the transmembrane domain interface. Comparison of different conformational structures reveals conformational changes, especially those of transmembrane helices and residues constituting the substrate translocation pathway during the cross-membrane transport process. Based on the structural data, a 'gate-flipper' translocation model of ABCG25-mediated ABA cross-membrane transport is proposed. Our structural data on AtABCG25 provide new clues to the physiological study of ABA and shed light on its potential applications in plants and agriculture.
History
DepositionJan 16, 2023-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35146.png

Downloads & links

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Map

FileDownload / File: emd_35146.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 210 pix.
= 249.9 Å		1.19 Å/pix.
x 210 pix.
= 249.9 Å		1.19 Å/pix.
x 210 pix.
= 249.9 Å

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Voxel sizeX=Y=Z: 1.19 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-5.6482096 - 8.089790000000001
Average (Standard dev.)0.00034439532 (±0.18370685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 249.90001 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpen map

Fileemd_35146_additional_1.map
Annotationunsharpen map
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Half map: #1

Fileemd_35146_half_map_1.map
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Half map: #2

Fileemd_35146_half_map_2.map
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Sample components

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Entire : Arabidopsis thaliana ABCG25

EntireName: Arabidopsis thaliana ABCG25
Components
  • Complex: Arabidopsis thaliana ABCG25
    • Protein or peptide: ABC transporter G family member 25
  • Ligand: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid

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Supramolecule #1: Arabidopsis thaliana ABCG25

SupramoleculeName: Arabidopsis thaliana ABCG25 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: ABC transporter G family member 25

MacromoleculeName: ABC transporter G family member 25 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 72.983867 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSAFDGVENQ MNGPDSSPRL SQDPREPRSL LSSSCFPITL KFVDVCYRVK IHGMSNDSCN IKKLLGLKQK PSDETRSTEE RTILSGVTG MISPGEFMAV LGPSGSGKST LLNAVAGRLH GSNLTGKILI NDGKITKQTL KRTGFVAQDD LLYPHLTVRE T LVFVALLR ...String:
MSAFDGVENQ MNGPDSSPRL SQDPREPRSL LSSSCFPITL KFVDVCYRVK IHGMSNDSCN IKKLLGLKQK PSDETRSTEE RTILSGVTG MISPGEFMAV LGPSGSGKST LLNAVAGRLH GSNLTGKILI NDGKITKQTL KRTGFVAQDD LLYPHLTVRE T LVFVALLR LPRSLTRDVK LRAAESVISE LGLTKCENTV VGNTFIRGIS GGERKRVSIA HELLINPSLL VLDEPTSGLD AT AALRLVQ TLAGLAHGKG KTVVTSIHQP SSRVFQMFDT VLLLSEGKCL FVGKGRDAMA YFESVGFSPA FPMNPADFLL DLA NGVCQT DGVTEREKPN VRQTLVTAYD TLLAPQVKTC IEVSHFPQDN ARFVKTRVNG GGITTCIATW FSQLCILLHR LLKE RRHES FDLLRIFQVV AASILCGLMW WHSDYRDVHD RLGLLFFISI FWGVLPSFNA VFTFPQERAI FTRERASGMY TLSSY FMAH VLGSLSMELV LPASFLTFTY WMVYLRPGIV PFLLTLSVLL LYVLASQGLG LALGAAIMDA KKASTIVTVT MLAFVL TGG YYVNKVPSGM VWMKYVSTTF YCYRLLVAIQ YGSGEEILRM LGCDSKGKQG ASAATSAGCR FVEEEVIGDV GMWTSVG VL FLMFFGYRVL AYLALRRIKH

UniProtKB: DUF1425 domain-containing protein

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Macromolecule #2: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl...

MacromoleculeName: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: A8S
Molecular weightTheoretical: 264.317 Da
Chemical component information

ChemComp-A8S:
(2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid / hormone*YM

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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: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 353594
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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