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- EMDB-37418: Cryo-EM structure of the ABCG25 bound to CHS -

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Basic information

Entry
Database: EMDB / ID: EMD-37418
TitleCryo-EM structure of the ABCG25 bound to CHS
Map data
Sample
  • Complex: Homodimer of ABCG25 bound to CHS
    • Protein or peptide: ABC transporter G family member 25
  • Ligand: CHOLESTEROL HEMISUCCINATE
Keywordsexporter / complex / transporter / 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: 3.1 Å
AuthorsXin J / Yan KG
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271251 China
CitationJournal: 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.
History
DepositionSep 9, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37418.png

Downloads & links

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Map

FileDownload / File: emd_37418.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-2.797333 - 4.082468
Average (Standard dev.)-0.0016578007 (±0.08016679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37418_msk_1.map
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Half map: #2

Fileemd_37418_half_map_1.map
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Half map: #1

Fileemd_37418_half_map_2.map
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Sample components

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Entire : Homodimer of ABCG25 bound to CHS

EntireName: Homodimer of ABCG25 bound to CHS
Components
  • Complex: Homodimer of ABCG25 bound to CHS
    • Protein or peptide: ABC transporter G family member 25
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Homodimer of ABCG25 bound to CHS

SupramoleculeName: Homodimer of ABCG25 bound to CHS / 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: 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: DUF1425 domain-containing protein

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Macromolecule #2: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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

Concentration6.8 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171268
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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