9WFQ | pdb_00009wfq

Structure of the wild-type ABCC2 dimer in Arabidopsis thaliana in the apo state

• PDB DOI: https://doi.org/10.2210/pdb9WFQ/pdb
• EM Map EMD-65935: EMDB EMDataResource

• Classification: PROTEIN TRANSPORT
• Organism(s): Arabidopsis thaliana
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-08-21 Released: 2025-12-24 
• Deposition Author(s): Sun, L., Liu, X., Qiu, X., Yang, Z., Gao, Y.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural insights into toxicant export mediated by ABCC2 in Arabidopsis thaliana.

Qiu, X., Yang, Z., Gao, Y., Sun, L., Liu, X.

(2025) Nat Commun 16: 11554-11554

• PubMed: 41430060 
• DOI: https://doi.org/10.1038/s41467-025-67713-5
• Primary Citation Related Structures: 
  9LI5, 9LI6, 9LI7, 9LI9, 9WFP, 9WFQ


• PubMed Abstract: 
  

  Plants are highly vulnerable to damage from environmental pollutants, making detoxification mechanisms essential for sustaining growth and development. ABCC2 in Arabidopsis thaliana (AtABCC2) plays a critical role in detoxification by exporting diverse toxic compounds. Here, we report the structures of AtABCC2 in three distinct states: substrate-free, bound to the substrate S-(2,4-dinitrophenyl)glutathione (DNP-GS), and bound to ATP. Both monomeric and dimeric forms of AtABCC2 are observed. Unlike other dimeric ABCC homologs, AtABCC2 features a dimer interface mediated by its transmembrane domains. DNP-GS occupies an amphipathic cavity formed by the transmembrane domains. ATP binding drives the conformational changes in each protomer which bring the transmembrane and nucleotide-binding domains closer together, transitioning the transporter from a cytosolic-facing to an occluded state. Together, these findings advance our understanding of the molecular basis of substrate binding and transport by AtABCC2, and shed light on plant detoxification mechanisms.

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Organizational Affiliation: 
• Department of Neurology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.
Department of Neurology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China. [e-mail].
Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China. [e-mail].
Department of Neurology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Physical Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China. [e-mail].
Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 364.62 kDa 
• Atom Count: 22,474 
• Modeled Residue Count: 2,844 
• Deposited Residue Count: 3,246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter C family member 2	A, B	1,623	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ABCC2, EST4, MRP2, At2g34660, T29F13.13 EC: 7.6.2.2
UniProt
Find proteins for Q42093 (Arabidopsis thaliana) Explore Q42093  Go to UniProtKB:  Q42093

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Sun, L., Liu, X., Qiu, X., Yang, Z., Gao, Y.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	32322041, 32321001, 31900885

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release
  
• Version 1.1: 2026-07-08
  Changes: Data collection, Database references