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- PDB-8zpx: Structure of the wild-type Arabidopsis ABCB1 in the apo state -

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Basic information

Entry
Database: PDB / ID: 8zpx
TitleStructure of the wild-type Arabidopsis ABCB1 in the apo state
ComponentsABC transporter B family member 1
KeywordsTRANSPORT PROTEIN / ABC transporter / wild-type / apo state
Function / homology
Function and homology information


anthocyanin accumulation in tissues in response to UV light / positive regulation of brassinosteroid mediated signaling pathway / response to red or far red light / auxin influx transmembrane transporter activity / stamen development / response to brassinosteroid / positive gravitropism / auxin export across the plasma membrane / auxin efflux transmembrane transporter activity / auxin polar transport ...anthocyanin accumulation in tissues in response to UV light / positive regulation of brassinosteroid mediated signaling pathway / response to red or far red light / auxin influx transmembrane transporter activity / stamen development / response to brassinosteroid / positive gravitropism / auxin export across the plasma membrane / auxin efflux transmembrane transporter activity / auxin polar transport / photomorphogenesis / response to auxin / response to blue light / auxin-activated signaling pathway / plasmodesma / response to nematode / regulation of cell size / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / plasma membrane
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 1
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)32322041; 32321001; 31900885 China
CitationJournal: Plant Commun / Year: 2025
Title: Structural insights into brassinosteroid export mediated by the Arabidopsis ABC transporter ABCB1.
Authors: Hong Wei / Heyuan Zhu / Wei Ying / Hilde Janssens / Miroslav Kvasnica / Johan M Winne / Yongxiang Gao / Jiří Friml / Qian Ma / Shutang Tan / Xin Liu / Eugenia Russinova / Linfeng Sun /
Abstract: Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant growth, development, and responses to environmental stresses. The export of bioactive BRs to the apoplast is essential for ...Brassinosteroids (BRs) are steroidal phytohormones indispensable for plant growth, development, and responses to environmental stresses. The export of bioactive BRs to the apoplast is essential for BR signaling initiation, which requires binding of a BR molecule to the extracellular domains of the plasma membrane-localized receptor complex. We have previously shown that the Arabidopsis thaliana ATP-binding cassette (ABC) transporter ABCB19 functions as a BR exporter and, together with its close homolog ABCB1, positively regulates BR signaling. Here, we demonstrate that ABCB1 is another BR transporter. The ATP hydrolysis activity of ABCB1 can be stimulated by bioactive BRs, and its transport activity was confirmed in proteoliposomes and protoplasts. Structures of ABCB1 were determined in substrate-unbound (apo), brassinolide (BL)-bound, and ATP plus BL-bound states. In the BL-bound structure, BL is bound to the hydrophobic cavity formed by the transmembrane domain and triggers local conformational changes. Together, our data provide additional insights into ABC transporter-mediated BR export.
History
DepositionMay 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ABC transporter B family member 1


Theoretical massNumber of molelcules
Total (without water)140,7291
Polymers140,7291
Non-polymers00
Water00
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 1 / ABC transporter ABCB.1 / AtABCB1 / Multidrug resistance protein 1 / P-glycoprotein 1 / AtPgp1


Mass: 140729.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABCB1, MDR1, PGP1, At2g36910, T1J8.9 / Production host: Homo sapiens (human) / Strain (production host): HEK293F / References: UniProt: Q9ZR72
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: Purified wild-type ABCB1 protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental 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 FIELD / 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: 277013 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0059233
ELECTRON MICROSCOPYf_angle_d0.75412496
ELECTRON MICROSCOPYf_dihedral_angle_d5.6141266
ELECTRON MICROSCOPYf_chiral_restr0.0451444
ELECTRON MICROSCOPYf_plane_restr0.0061587

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