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- PDB-9jup: Structure of Arabidopsis thaliana ABCB1 with AMP-PNP bound in the... -

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Basic information

Entry
Database: PDB / ID: 9jup
TitleStructure of Arabidopsis thaliana ABCB1 with AMP-PNP bound in the outward-facing conformation
ComponentsABC transporter B family member 1
KeywordsTRANSPORT PROTEIN / ABCB1 / auxin transport / brassinolide (BL) transport
Function / homology
Function and homology information


auxin influx transmembrane transporter activity / anthocyanin accumulation in tissues in response to UV light / response to red or far red light / auxin export across the plasma membrane / stamen development / positive gravitropism / auxin efflux transmembrane transporter activity / auxin polar transport / response to blue light / photomorphogenesis ...auxin influx transmembrane transporter activity / anthocyanin accumulation in tissues in response to UV light / response to red or far red light / auxin export across the plasma membrane / stamen development / positive gravitropism / auxin efflux transmembrane transporter activity / auxin polar transport / response to blue light / photomorphogenesis / response to auxin / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ABC transporter B family member 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChen, Q. / Su, N. / Guo, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32400995 China
CitationJournal: Structure / Year: 2025
Title: Structures and mechanisms of the ABC transporter ABCB1 from Arabidopsis thaliana.
Authors: Qian Chen / Li Zhu / Sufen Zhang / Shuai Qiao / Zhong Jie Ding / Shao Jian Zheng / Jiangtao Guo / Nannan Su /
Abstract: The Arabidopsis thaliana auxin transporter ABCB1 plays a fundamental role in the regulation of plant growth and development. While its homolog ABCB19 was previously shown to transport ...The Arabidopsis thaliana auxin transporter ABCB1 plays a fundamental role in the regulation of plant growth and development. While its homolog ABCB19 was previously shown to transport brassinosteroids (BR), another class of essential hormones, the ability of ABCB1 to mediate BR transport has remained unexplored. In this study we show that ABCB1 also transports brassinosteroids with an in vitro brassinolide (BL) transport assay. Using single-particle cryo-electron microscopy, we determined ABCB1 structures in multiple inward-facing conformations in the apo state, ANP-bound state, BL-bound state, and the both BL- and ANP-bound state. BL binds to the large cavity of two transmembrane domains, inducing a slight conformational change. Additionally, we obtained the structure of ABCB1 in an outward-facing conformation. By comparing these different conformations, we elucidated the possible mechanism of hormone transport by ABCB1. These high-resolution structures help us to understand the structural basis for hormone recognition and transport mechanisms of ABCB1.
History
DepositionOct 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
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Revision 1.1Mar 19, 2025Group: Data collection / Database references / Structure summary
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter B family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,3805
Polymers145,3191
Non-polymers1,0614
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: 145318.953 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 / Cell line (production host): HEK 293S GnTl- / Production host: Homo sapiens (human) / References: UniProt: Q9ZR72
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
Has ligand of interestY
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: Structure of Arabidopsis thaliana ABCB1 with AMP-PNP bound in the outward-facing conformation
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingAverage exposure time: 3.42 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46629 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028815
ELECTRON MICROSCOPYf_angle_d0.48211948
ELECTRON MICROSCOPYf_dihedral_angle_d5.2031215
ELECTRON MICROSCOPYf_chiral_restr0.0381375
ELECTRON MICROSCOPYf_plane_restr0.0031505

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