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- PDB-9u56: Cryo-EM structure of AtABCC2 in apo form -

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Basic information

Entry
Database: PDB / ID: 9u56
TitleCryo-EM structure of AtABCC2 in apo form
ComponentsABC transporter C family member 2
KeywordsTRANSPORT PROTEIN / ABC transporter / Transmembrane 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
CHOLESTEROL / ABC transporter C family member 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsDong, J.Q. / Yang, T.-L. / Yang, G.-F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of AtABCC2 in apo form
Authors: Dong, J.Q. / Yang, T.-L. / Yang, G.-F.
History
DepositionMar 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / 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)185,4049
Polymers182,3111
Non-polymers3,0938
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: 182310.922 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-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H46O / 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 from Arabidopsis thaliana / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 recordingAverage exposure time: 4.66 sec. / Electron dose: 49.72 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2286911
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 336481 / Symmetry type: POINT

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