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- EMDB-63113: Structure of ABCC2(E1404Q) in Arabidopsis thaliana in the apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-63113
TitleStructure of ABCC2(E1404Q) in Arabidopsis thaliana in the apo state
Map data
Sample
  • Complex: substrate unbound ABCC2(E1404Q) dimer
    • Protein or peptide: ABC transporter C family member 2
KeywordsPlant detoxification effect / Transporter / ABCC2 protein / TRANSPORT 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
ABC transporter C family member 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsSun L / Liu X / Yang Z / Gao Y / Qiu X
Funding support China, 1 items
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
DepositionJan 13, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63113.png

Downloads & links

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Map

FileDownload / File: emd_63113.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.582547 - 2.7393622
Average (Standard dev.)0.0067683975 (±0.0783488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63113_msk_1.map
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Half map: #2

Fileemd_63113_half_map_1.map
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Half map: #1

Fileemd_63113_half_map_2.map
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Sample components

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Entire : substrate unbound ABCC2(E1404Q) dimer

EntireName: substrate unbound ABCC2(E1404Q) dimer
Components
  • Complex: substrate unbound ABCC2(E1404Q) dimer
    • Protein or peptide: ABC transporter C family member 2

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Supramolecule #1: substrate unbound ABCC2(E1404Q) dimer

SupramoleculeName: substrate unbound ABCC2(E1404Q) dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: ABC transporter C family member 2

MacromoleculeName: ABC transporter C family member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type xenobiotic transporter
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 182.309938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGFEFIEWYC KPVPNGVWTK QVANAFGAYT PCATDSFVLG ISQLVLLVLC LYRIWLALKD HKVERFCLRS RLYNYFLALL AAYATAEPL FRLIMGISVL DFDGPGLPPF EAFGLGVKAF AWGAVMVMIL METKIYIREL RWYVRFAVIY ALVGDMVLLN L VLSVKEYY ...String:
MGFEFIEWYC KPVPNGVWTK QVANAFGAYT PCATDSFVLG ISQLVLLVLC LYRIWLALKD HKVERFCLRS RLYNYFLALL AAYATAEPL FRLIMGISVL DFDGPGLPPF EAFGLGVKAF AWGAVMVMIL METKIYIREL RWYVRFAVIY ALVGDMVLLN L VLSVKEYY SSYVLYLYTS EVGAQVLFGI LLFMHLPNLD TYPGYMPVRS ETVDDYEYEE ISDGQQICPE KHANIFDKIF FS WMNPLMT LGSKRPLTEK DVWYLDTWDQ TETLFTSFQH SWDKELQKPQ PWLLRALNNS LGGRFWWGGF WKIGNDCSQF VGP LLLNQL LKSMQEDAPA WMGYIYAFSI FVGVVFGVLC EAQYFQNVMR VGYRLRSALI AAVFRKSLRL TNEGRRKFQT GKIT NLMTT DAESLQQICQ SLHTMWSAPF RIIIALILLY QQLGVASLIG ALLLVLMFPL QTVIISKMQK LTKEGLQRTD KRIGL MNEV LAAMDTVKCY AWENSFQSKV QTVRDDELSW FRKSQLLGAL NMFILNSIPV LVTIVSFGVF TLLGGDLTPA RAFTSL SLF AVLRFPLFML PNIITQVVNA NVSLKRLEEV LATEERILLP NPPIEPGEPA ISIRNGYFSW DSKGDRPTLS NINLDVP LG SLVAVVGSTG EGKTSLISAI LGELPATSDA IVTLRGSVAY VPQVSWIFNA TVRDNILFGS PFDREKYERA IDVTSLKH D LELLPGGDLT EIGERGVNIS GGQKQRVSMA RAVYSNSDVY IFDDPLSALD AHVGQQVFEK CIKRELGQKT RVLVTNQLH FLSQVDRIVL VHEGTVKEEG TYEELSSNGP LFQRLMENAG KVEEYSEENG EAEADQTAEQ PVANGNTNGL QMDGSDDKKS KEGNKKGGK SVLIKQEERE TGVVSWRVLK RYQDALGGAW VVMMLLLCYV LTEVFRVTSS TWLSEWTDAG TPKSHGPLFY N LIYALLSF GQVLVTLTNS YWLIMSSLYA AKKLHDNMLH SILRAPMSFF HTNPLGRIIN RFAKDLGDID RTVAVFVNMF MG QVSQLLS TVVLIGIVST LSLWAIMPLL VLFYGAYLYY QNTAREVKRM DSISRSPVYA QFGEALNGLS TIRAYKAYDR MAD INGRSM DNNIRFTLVN MGANRWLGIR LETLGGLMIW LTASFAVMQN GRAENQQAFA STMGLLLSYA LNITSLLTGV LRLA SLAEN SLNAVERVGN YIEIPPEAPP VIENNRPPPG WPSSGSIKFE DVVLRYRPQL PPVLHGVSFF IHPTDKVGIV GRTGA GKSS LLNALFRIVE VEKGRILIDD CDVGKFGLMD LRKVLGIIPQ SPVLFSGTVR FNLDPFGEHN DADLWESLER AHLKDT IRR NPLGLDAEVS EAGENFSVGQ RQLLSLSRAL LRRSKILVLD QATAAVDVRT DALIQKTIRE EFKSCTMLII AHRLNTI ID CDKILVLDSG RVQEFSSPEN LLSNEGSSFS KMVQSTGAAN AEYLRSLVLD NKRAKDDSHH LQGQRKWLAS SRWAAAAQ F ALAASLTSSH NDLQSLEIED DSSILKRTND AVVTLRSVLE GKHDKEIAES LEEHNISREG WLSSLYRMVE GLAVMSRLA RNRMQQPDYN FEGNTFDWDN VEM

UniProtKB: ABC transporter C family member 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 106893
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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