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- PDB-9wfp: Structure of ABCC2(E1404Q) monomer in Arabidopsis thaliana in the... -

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Basic information

Entry
Database: PDB / ID: 9wfp
TitleStructure of ABCC2(E1404Q) monomer in Arabidopsis thaliana in the DNP-GS bound state
ComponentsABC transporter C family member 2
KeywordsPROTEIN TRANSPORT / Plant detoxification effect / Transporter / ABCC2 protein
Function / homology
Function and homology information


(+)-abscisic acid D-glucopyranosyl ester transmembrane transporter activity / (+)-abscisic acid D-glucopyranosyl ester transmembrane transport / plant-type vacuole / vacuole / ABC-type xenobiotic transporter / vacuolar membrane / ABC-type xenobiotic transporter activity / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / calmodulin binding ...(+)-abscisic acid D-glucopyranosyl ester transmembrane transporter activity / (+)-abscisic acid D-glucopyranosyl ester transmembrane transport / plant-type vacuole / vacuole / ABC-type xenobiotic transporter / vacuolar membrane / ABC-type xenobiotic transporter activity / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / calmodulin binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding
Similarity search - Function
ABC transporter C family, six-transmembrane helical domain 2 / ABC transporter C family, six-transmembrane helical domain 1 / : / 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 C family, six-transmembrane helical domain 2 / ABC transporter C family, six-transmembrane helical domain 1 / : / 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
GLUTATHIONE S-(2,4 DINITROBENZENE) / ABC transporter C family member 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsSun, L. / Liu, X. / Qiu, X. / Yang, Z. / Gao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32322041, 32321001, 31900885 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into toxicant export mediated by ABCC2 in Arabidopsis thaliana.
Authors: Xuan Qiu / Zhisen Yang / Yongxiang Gao / Linfeng Sun / Xin Liu /
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 ...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.
History
DepositionAug 21, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter C family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,7832
Polymers182,3101
Non-polymers4731
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 C family member 2 / ABC transporter ABCC.2 / AtABCC2 / ATP-energized glutathione S-conjugate pump 2 / Glutathione S- ...ABC transporter ABCC.2 / AtABCC2 / ATP-energized glutathione S-conjugate pump 2 / Glutathione S-conjugate-transporting ATPase 2 / Multidrug resistance-associated protein 2


Mass: 182309.938 Da / Num. of mol.: 1 / Mutation: E1404Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABCC2, EST4, MRP2, At2g34660, T29F13.13 / Production host: Homo sapiens (human) / Strain (production host): HEK293F
References: UniProt: Q42093, ABC-type xenobiotic transporter
#2: Chemical ChemComp-GDN / GLUTATHIONE S-(2,4 DINITROBENZENE)


Mass: 473.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N5O10S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: ABCC2 monomer / 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: OTHER
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 software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.13_2998:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59944 / Symmetry type: POINT
Atomic model buildingPDB-ID: 9LI6

9li6


Accession code: 9LI6 / Source name: PDB / Type: experimental model

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