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- EMDB-63114: Structure of ABCC2(E1404Q) in Arabidopsis thaliana in the ATP bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-63114
TitleStructure of ABCC2(E1404Q) in Arabidopsis thaliana in the ATP bound state
Map data
Sample
  • Complex: ATP bound ABCC2(E1404Q) dimer
    • Protein or peptide: ABC transporter C family member 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
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 / calmodulin binding / endoplasmic reticulum ...(+)-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 / 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: 3.42 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: To Be Published
Title: Structure of ABCC2(E1404Q) in Arabidopsis thaliana in the ATP bound state
Authors: Sun L / Liu X / Yang Z / Gao Y / Qiu X
History
DepositionJan 13, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63114.png

Downloads & links

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Map

FileDownload / File: emd_63114.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.53
Minimum - Maximum-1.4291248 - 2.5543008
Average (Standard dev.)0.010324831 (±0.09720867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63114_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63114_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63114_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATP bound ABCC2(E1404Q) dimer

EntireName: ATP bound ABCC2(E1404Q) dimer
Components
  • Complex: ATP bound ABCC2(E1404Q) dimer
    • Protein or peptide: ABC transporter C family member 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ATP bound ABCC2(E1404Q) dimer

SupramoleculeName: ATP bound ABCC2(E1404Q) dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53221
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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