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- PDB-9kg2: Cryo-EM structure of apo form atABCB19 in lipid nanodisc -

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Basic information

Entry
Database: PDB / ID: 9kg2
TitleCryo-EM structure of apo form atABCB19 in lipid nanodisc
ComponentsABC transporter B family member 19
KeywordsMEMBRANE PROTEIN / ABCB19 / Plant hormone transport / apo form
Function / homology
Function and homology information


acropetal auxin transport / formation of plant organ boundary / basipetal auxin transport / auxin transport / anthocyanin accumulation in tissues in response to UV light / positive regulation of brassinosteroid mediated signaling pathway / response to red or far red light / lateral root development / stamen development / response to brassinosteroid ...acropetal auxin transport / formation of plant organ boundary / basipetal auxin transport / auxin transport / anthocyanin accumulation in tissues in response to UV light / positive regulation of brassinosteroid mediated signaling pathway / response to red or far red light / lateral root development / stamen development / response to brassinosteroid / positive gravitropism / auxin export across the plasma membrane / auxin efflux transmembrane transporter activity / response to far red light / auxin polar transport / root development / photomorphogenesis / response to auxin / response to blue light / auxin-activated signaling pathway / regulation of cell size / ABC-type transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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 B family member 19
Similarity search - Component
Biological speciesArabidopsis thaliana x Arabidopsis lyrata (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLiu, Y. / Liao, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2025
Title: Conformational cycle and small-molecule inhibition mechanism of a plant ABCB transporter in lipid membranes.
Authors: Yong Liu / Maofu Liao /
Abstract: In plants, ATP-binding cassette (ABC) transporters are crucial for nutrient uptake, phytohormone transport, and environmental response. It is of great interest to understand the mechanisms of these ...In plants, ATP-binding cassette (ABC) transporters are crucial for nutrient uptake, phytohormone transport, and environmental response. It is of great interest to understand the mechanisms of these transporters and develop small-molecule modulators to regulate plant growth. ABCB19 was recently shown to transport brassinosteroid, shaping hormone dynamics and plant architecture. However, the conformational cycle and inhibitor mechanism of ABCB transporters remain elusive. We reconstituted ABCB19 into lipid nanodiscs, where activity was drastically higher than in detergents, and determined its cryo-electron microscopy structures in substrate-free, substrate-bound, vanadate-trapped, and inhibitor-bound states. Inward-facing ABCB19 moved inward upon substrate binding and fully closed with vanadate trapping, unexpectedly temperature dependent. Two inhibitor molecules locked ABCB19 in the inward-facing conformation. Mutagenesis identified key residues for substrate and inhibitor binding, revealing differential contributions to transporter function and inhibition. These results deepen knowledge of plant ABCB transporters, laying a foundation for targeted manipulation to enhance plant resilience and productivity.
History
DepositionNov 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0May 21, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: ABC transporter B family member 19


Theoretical massNumber of molelcules
Total (without water)136,9331
Polymers136,9331
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ABC transporter B family member 19 / ABC transporter ABCB.19 / AtABCB19 / Multidrug resistance protein 11 / P-glycoprotein 19


Mass: 136932.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Arabidopsis thaliana x Arabidopsis lyrata is not available at the time of biocuration. Current sequence reference is from UniProt id Q9LJX0.
Source: (gene. exp.) Arabidopsis thaliana x Arabidopsis lyrata (thale cress)
Gene: ABCB19, MDR1, MDR11, PGP19, At3g28860, MLD15.2 / Production host: Homo sapiens (human) / References: UniProt: Q9LJX0
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Apo form atABCB19 in lipid nanodisc / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.13679 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.8 / Details: 20mM Tris-HCl,pH 7.8, 150mM NaCl
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157216 / Symmetry type: POINT

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