9JUL | pdb_00009jul

Structure of Arabidopsis thaliana ABCB1 with brassinolide bound in the inward-facing conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9JUL

This is version 1.2 of the entry. See complete history

Literature

Structures and mechanisms of the ABC transporter ABCB1 from Arabidopsis thaliana.

Chen, Q.Zhu, L.Zhang, S.Qiao, S.Ding, Z.J.Zheng, S.J.Guo, J.Su, N.

(2025) Structure 33: 903-915.e5

  • DOI: https://doi.org/10.1016/j.str.2025.02.008
  • Primary Citation Related Structures: 
    9JUJ, 9JUK, 9JUL, 9JUM, 9JUN, 9JUO, 9JUP

  • PubMed 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 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.


  • Organizational Affiliation
    • Center for Membrane Receptors and Brain Medicine, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang 322000, China; Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China; Nanhu Brain-computer Interface Institute, Hangzhou, Zhejiang 311100, China.

Macromolecule Content 

  • Total Structure Weight: 145.8 kDa 
  • Atom Count: 9,005 
  • Modeled Residue Count: 1,165 
  • Deposited Residue Count: 1,327 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ABC transporter B family member 11,327Arabidopsis thalianaMutation(s): 0 
Gene Names: ABCB1MDR1PGP1At2g36910T1J8.9
Membrane Entity: Yes 
UniProt
Find proteins for Q9ZR72 (Arabidopsis thaliana)
Explore Q9ZR72 
Go to UniProtKB:  Q9ZR72
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZR72
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BLD
(Subject of Investigation/LOI)

Query on BLD



Download:Ideal Coordinates CCD File
B [auth A]Brassinolide
C28 H48 O6
IXVMHGVQKLDRKH-KNBKMWSGSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32400995

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-03-19
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-05-14
    Changes: Data collection, Database references