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- PDB-8wom: Structure of the wild-type Arabidopsis ABCB19 in the brassinolide... -

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Basic information

Entry
Database: PDB / ID: 8wom
TitleStructure of the wild-type Arabidopsis ABCB19 in the brassinolide-bound state
ComponentsABC transporter B family member 19
KeywordsTRANSPORT PROTEIN / ABC transporter / wild-type / brassinolide-bound state
Function / homology
Function and homology information


acropetal auxin transport / anthocyanin accumulation in tissues in response to UV light / response to red or far red light / formation of plant organ boundary / basipetal auxin transport / auxin transport / auxin efflux transmembrane transporter activity / positive gravitropism / stamen development / auxin polar transport ...acropetal auxin transport / anthocyanin accumulation in tissues in response to UV light / response to red or far red light / formation of plant organ boundary / basipetal auxin transport / auxin transport / auxin efflux transmembrane transporter activity / positive gravitropism / stamen development / auxin polar transport / lateral root development / response to far red light / photomorphogenesis / response to blue light / root development / response to auxin / 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
Brassinolide / ABC transporter B family member 19
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYing, W. / Wei, H. / Liu, X. / Sun, L.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020103 China
National Natural Science Foundation of China (NSFC)31900885; 31870732; 32322041 China
CitationJournal: Science / Year: 2024
Title: Structure and function of the ABC transporter ABCB19 in brassinosteroid export.
Authors: Wei Ying / Yaowei Wang / Hong Wei / Yongming Luo / Qian Ma / Heyuan Zhu / Hilde Janssens / Nemanja Vukašinović / Miroslav Kvasnica / Johan M Winne / Yongxiang Gao / Shutang Tan / Jiří ...Authors: Wei Ying / Yaowei Wang / Hong Wei / Yongming Luo / Qian Ma / Heyuan Zhu / Hilde Janssens / Nemanja Vukašinović / Miroslav Kvasnica / Johan M Winne / Yongxiang Gao / Shutang Tan / Jiří Friml / Xin Liu / Eugenia Russinova / Linfeng Sun /
Abstract: Brassinosteroids are steroidal phytohormones that regulate plant development and physiology, including adaptation to environmental stresses. Brassinosteroids are synthesized in the cell interior but ...Brassinosteroids are steroidal phytohormones that regulate plant development and physiology, including adaptation to environmental stresses. Brassinosteroids are synthesized in the cell interior but bind receptors at the cell surface, necessitating a yet to be identified export mechanism. Here, we show that a member of the ATP-binding cassette (ABC) transporter superfamily, ABCB19, functions as a brassinosteroid exporter. We present its structure in both the substrate-unbound and the brassinosteroid-bound states. Bioactive brassinosteroids are potent activators of ABCB19 ATP hydrolysis activity, and transport assays showed that ABCB19 transports brassinosteroids. In , ABCB19 and its close homolog, ABCB1, positively regulate brassinosteroid responses. Our results uncover an elusive export mechanism for bioactive brassinosteroids that is tightly coordinated with brassinosteroid signaling.
History
DepositionOct 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter B family member 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,4132
Polymers136,9331
Non-polymers4811
Water0
1


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

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Components

#1: Protein ABC transporter B family member 19


Mass: 136932.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABCB19 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9LJX0
#2: Chemical ChemComp-BLD / Brassinolide / (3aS,5S,6R,7aR,7bS,9aS,10R,12aS,12bS)-10-[(2S,3R,4R,5S)-3,4-dihydroxy-5,6-dimethylheptan-2-yl]-5,6-dihydroxy-7a,9a-dime thylhexadecahydro-3H-benzo[c]indeno[5,4-e]oxepin-3-one / Brassinolide


Mass: 480.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H48O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
Has ligand of interestY

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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: Purified wild-type ABCB19 protein in complex with brassinolide
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.13_2998: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 347545 / Symmetry type: POINT

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