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- EMDB-37455: Cryo-EM structure of the ABCG25 -

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Basic information

Entry
Database: EMDB / ID: EMD-37455
TitleCryo-EM structure of the ABCG25
Map data
Sample
  • Complex: Cryo-EM structure of the ABCG25
    • Protein or peptide: ABC transporter G family member 25
Keywordsexporter / complex / transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


intercellular transport / negative regulation of post-embryonic development / abscisic acid transport / export from cell / response to abscisic acid / abscisic acid-activated signaling pathway / efflux transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / response to cold ...intercellular transport / negative regulation of post-embryonic development / abscisic acid transport / export from cell / response to abscisic acid / abscisic acid-activated signaling pathway / efflux transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / response to cold / transmembrane transport / response to heat / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter family G domain / ABC-2 type transporter / ABC-2 type transporter / ABC-2 type transporter / 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 25
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsXin J / Yan KG
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271251 China
Citation
Journal: Plant Commun / Year: 2024
Title: Structural insights into AtABCG25, an angiosperm-specific abscisic acid exporter.
Authors: Jian Xin / Yeling Zhou / Yichun Qiu / He Geng / Yuzhu Wang / Yi Song / Jiansheng Liang / Kaige Yan /
Abstract: Cellular hormone homeostasis is essential for precise spatial and temporal signaling responses and plant fitness. Abscisic acid (ABA) plays pivotal roles in orchestrating various developmental and ...Cellular hormone homeostasis is essential for precise spatial and temporal signaling responses and plant fitness. Abscisic acid (ABA) plays pivotal roles in orchestrating various developmental and stress responses and confers fitness benefits over ecological and evolutionary timescales in terrestrial plants. Cellular ABA level is regulated by complex processes, including biosynthesis, catabolism, and transport. AtABCG25 is the first ABA exporter identified through genetic screening and affects diverse ABA responses. Resolving the structural basis of ABA export by ABCG25 is critical for further manipulations of ABA homeostasis and plant fitness. We used cryo-electron microscopy to elucidate the structural dynamics of AtABCG25 and successfully characterized different states, including apo AtABCG25, ABA-bound AtABCG25, and ATP-bound AtABCG25 (E232Q). Notably, AtABCG25 forms a homodimer that features a deep, slit-like cavity in the transmembrane domain, and we precisely characterized the critical residues in the cavity where ABA binds. ATP binding triggers closure of the nucleotide-binding domains and conformational transitions in the transmembrane domains. We show that AtABCG25 belongs to a conserved ABCG subfamily that originated during the evolution of angiosperms. This subfamily neofunctionalized to regulate seed germination via the endosperm, in concert with the evolution of this angiosperm-specific, embryo-nourishing tissue. Collectively, these findings provide valuable insights into the intricate substrate recognition and transport mechanisms of the ABA exporter AtABCG25, paving the way for genetic manipulation of ABA homeostasis and plant fitness.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Xin J / Yan KG
History
DepositionSep 14, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37455.png

Downloads & links

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Map

FileDownload / File: emd_37455.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.095 Å
Density
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-2.6103854 - 3.7376032
Average (Standard dev.)-0.003714913 (±0.07464298)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 280.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37455_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

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Half map: #2

Fileemd_37455_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37455_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of the ABCG25

EntireName: Cryo-EM structure of the ABCG25
Components
  • Complex: Cryo-EM structure of the ABCG25
    • Protein or peptide: ABC transporter G family member 25

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Supramolecule #1: Cryo-EM structure of the ABCG25

SupramoleculeName: Cryo-EM structure of the ABCG25 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 77.121148 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDHDGDY KDHDIDYKDD DDKGSDLEVL FQGPGSMSAF DGVENQMNGP DSSPRLSQDP REPRSLLSSS CFPITLKFVD VCYRVKIHG MSNDSCNIKK LLGLKQKPSD ETRSTEERTI LSGVTGMISP GEFMAVLGPS GSGKSTLLNA VAGRLHGSNL T GKILINDG ...String:
MDYKDHDGDY KDHDIDYKDD DDKGSDLEVL FQGPGSMSAF DGVENQMNGP DSSPRLSQDP REPRSLLSSS CFPITLKFVD VCYRVKIHG MSNDSCNIKK LLGLKQKPSD ETRSTEERTI LSGVTGMISP GEFMAVLGPS GSGKSTLLNA VAGRLHGSNL T GKILINDG KITKQTLKRT GFVAQDDLLY PHLTVRETLV FVALLRLPRS LTRDVKLRAA ESVISELGLT KCENTVVGNT FI RGISGGE RKRVSIAHEL LINPSLLVLD EPTSGLDATA ALRLVQTLAG LAHGKGKTVV TSIHQPSSRV FQMFDTVLLL SEG KCLFVG KGRDAMAYFE SVGFSPAFPM NPADFLLDLA NGVCQTDGVT EREKPNVRQT LVTAYDTLLA PQVKTCIEVS HFPQ DNARF VKTRVNGGGI TTCIATWFSQ LCILLHRLLK ERRHESFDLL RIFQVVAASI LCGLMWWHSD YRDVHDRLGL LFFIS IFWG VLPSFNAVFT FPQERAIFTR ERASGMYTLS SYFMAHVLGS LSMELVLPAS FLTFTYWMVY LRPGIVPFLL TLSVLL LYV LASQGLGLAL GAAIMDAKKA STIVTVTMLA FVLTGGYYVN KVPSGMVWMK YVSTTFYCYR LLVAIQYGSG EEILRML GC DSKGKQGASA ATSAGCRFVE EEVIGDVGMW TSVGVLFLMF FGYRVLAYLA LRRIKH

UniProtKB: ABC transporter G family member 25

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5625 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87677
FSC plot (resolution estimation)

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