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- PDB-9wet: Cryo-EM structure of AtABCC2 in ATP-bound, outward-facing state -

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Basic information

Entry
Database: PDB / ID: 9wet
TitleCryo-EM structure of AtABCC2 in ATP-bound, outward-facing state
ComponentsABC transporter C family member 2
KeywordsTRANSPORT PROTEIN / Membrane transporter / Complex
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
ADENOSINE-5'-TRIPHOSPHATE / CHOLESTEROL / ABC transporter C family member 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsDong, J. / Yang, T.-L. / Lin, H.-Y. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Discov / Year: 2026
Title: Molecular basis of Arabidopsis ABCC2 in plant detoxification.
Authors: Jiangqing Dong / Tai-Li Yang / Xin-He Yu / Ke-Xin Hu / Lin-Po Xu / Yuan-Guang Jiang / Hong-Yan Lin / Guang-Fu Yang /
History
DepositionAug 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: 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)185,69311
Polymers182,3101
Non-polymers3,38310
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ABCC2, EST4, MRP2, At2g34660, T29F13.13 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q42093, ABC-type xenobiotic transporter
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H46O
Has ligand of interestN
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: AtABCC2 in complex with ATP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50.1 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 5989

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7UCSF Chimeramodel fitting
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1012661
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180748 / Symmetry type: POINT
RefinementHighest resolution: 2.85 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311805
ELECTRON MICROSCOPYf_angle_d0.69716097
ELECTRON MICROSCOPYf_dihedral_angle_d10.4881809
ELECTRON MICROSCOPYf_chiral_restr0.0461876
ELECTRON MICROSCOPYf_plane_restr0.0041966

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