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- EMDB-63865: Cryo-EM structure of dimeric AtABCC2 -

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Basic information

Entry
Database: EMDB / ID: EMD-63865
TitleCryo-EM structure of dimeric AtABCC2
Map data
Sample
  • Organelle or cellular component: ABCC2
    • Protein or peptide: ABC transporter C family member 2
  • Ligand: CHOLESTEROL
  • Ligand: HEXADECANE
KeywordsABC Transporter / ATPase / 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: 3.42 Å
AuthorsYang G-F / Dong JQ / Yang T-L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of dimeric AtABCC2
Authors: Yang G-F / Dong JQ / Yang T-L
History
DepositionMar 20, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63865.png

Downloads & links

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Map

FileDownload / File: emd_63865.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.053296 - 1.1035058
Average (Standard dev.)0.0031520654 (±0.03237248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63865_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63865_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 : ABCC2

EntireName: ABCC2
Components
  • Organelle or cellular component: ABCC2
    • Protein or peptide: ABC transporter C family member 2
  • Ligand: CHOLESTEROL
  • Ligand: HEXADECANE

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Supramolecule #1: ABCC2

SupramoleculeName: ABCC2 / type: organelle_or_cellular_component / 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: 164.383156 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EFIEWYCKPV PNGVWTKQVA NAFGAYTPCA TDSFVLGISQ LVLLVLCLYR IWLALKDHKV ERFCLRSRLY NYFLALLAAY ATAEPLFRL IMGISVLDFD GPGLPPFEAF GLGVKAFAWG AVMVMILMET KIYIRELRWY VRFAVIYALV GDMVLLNLVL S VKEYYSSY ...String:
EFIEWYCKPV PNGVWTKQVA NAFGAYTPCA TDSFVLGISQ LVLLVLCLYR IWLALKDHKV ERFCLRSRLY NYFLALLAAY ATAEPLFRL IMGISVLDFD GPGLPPFEAF GLGVKAFAWG AVMVMILMET KIYIRELRWY VRFAVIYALV GDMVLLNLVL S VKEYYSSY VLYLYTSEVG AQVLFGILLF MHLPNLDTYP GYMPVRSETV DDYEYEEISD GQQICPEKHA NIFDKIFFSW MN PLMTLGS KRPLTEKDVW YLDTWDQTET LFTSFQHSWD KELQKPQPWL LRALNNSLGG RFWWGGFWKI GNDCSQFVGP LLL NQLLKS MQEDAPAWMG YIYAFSIFVG VVFGVLCEAQ YFQNVMRVGY RLRSALIAAV FRKSLRLTNE GRRKFQTGKI TNLM TTDAE SLQQICQSLH TMWSAPFRII IALILLYQQL GVASLIGALL LVLMFPLQTV IISKMQKLTK EGLQRTDKRI GLMNE VLAA MDTVKCYAWE NSFQSKVQTV RDDELSWFRK SQLLGALNMF ILNSIPVLVT IVSFGVFTLL GGDLTPARAF TSLSLF AVL RFPLFMLPNI ITQVVNANVS LKRLEEVLAT EERILLPNPP IEPGEPAISI RNGYFSWDSK GDRPTLSNIN LDVPLGS LV AVVGSTGEGK TSLISAILGE LPATSDAIVT LRGSVAYVPQ VSWIFNATVR DNILFGSPFD REKYERAIDV TSLKHDLE L LPGGDLTEIG ERGVNISGGQ KQRVSMARAV YSNSDVYIFD DPLSALDAHV GQQVFEKCIK RELGQKTRVL VTNQLHFLS QVDRIVLVHE GTVKEEGTYE ELSSNGPLFQ RLMENAGKVE EYSEENGEAE ADQTAEQPVA NGNTNGLQMD GSDDKKSKEG NKKGGKSVL IKQEERETGV VSWRVLKRYQ DALGGAWVVM MLLLCYVLTE VFRVTSSTWL SEWTDAGTPK SHGPLFYNLI Y ALLSFGQV LVTLTNSYWL IMSSLYAAKK LHDNMLHSIL RAPMSFFHTN PLGRIINRFA KDLGDIDRTV AVFVNMFMGQ VS QLLSTVV LIGIVSTLSL WAIMPLLVLF YGAYLYYQNT AREVKRMDSI SRSPVYAQFG EALNGLSTIR AYKAYDRMAD ING RSMDNN IRFTLVNMGA NRWLGIRLET LGGLMIWLTA SFAVMQNGRA ENQQAFASTM GLLLSYALNI TSLLTGVLRL ASLA ENSLN AVERVGNYIE IPPEAPPVIE NNRPPPGWPS SGSIKFEDVV LRYRPQLPPV LHGVSFFIHP TDKVGIVGRT GAGKS SLLN ALFRIVEVEK GRILIDDCDV GKFGLMDLRK VLGIIPQSPV LFSGTVRFNL DPFGEHNDAD LWESLERAHL KDTIRR NPL GLDAEVSEAG ENFSVGQRQL LSLSRALLRR SKILVLDEAT AAVDVRTDAL IQKTIREEFK SCTMLIIAHR LNTIIDC DK ILVLDSGRVQ EFSSPENLLS NE

UniProtKB: ABC transporter C family member 2

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 10 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 3 / Number of copies: 2 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 49.72 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 39873
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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