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- EMDB-65951: Cryo-EM structure of 2,4-DB-CoA-bound Arabidopsis thaliana fatty ... -

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Basic information

Entry
Database: EMDB / ID: EMD-65951
TitleCryo-EM structure of 2,4-DB-CoA-bound Arabidopsis thaliana fatty acid transporter CTS
Map data
Sample
  • Complex: Arabidopsis thaliana fatty acid transporter CTS
    • Protein or peptide: ABC transporter D family member 1
  • Ligand: ~{S}-[2-[3-[[(2~{S})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 4-[2,4-bis(chloranyl)phenoxy]butanethioate
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsABC transporter / fatty acid transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


ABC-type fatty-acyl-CoA transporter / fatty-acyl-CoA transport / glyoxysomal membrane / positive regulation of seed germination / ABC-type fatty-acyl-CoA transporter activity / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / peroxisome organization / ubiquinone biosynthetic process / peroxisomal membrane ...ABC-type fatty-acyl-CoA transporter / fatty-acyl-CoA transport / glyoxysomal membrane / positive regulation of seed germination / ABC-type fatty-acyl-CoA transporter activity / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / peroxisome organization / ubiquinone biosynthetic process / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / fatty acid beta-oxidation / ATPase-coupled transmembrane transporter activity / lipid catabolic process / peroxisome / ATP hydrolysis activity / ATP binding
Similarity search - Function
ABC transporter transmembrane region 2 / : / 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. ...ABC transporter transmembrane region 2 / : / 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 D family member 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZha ZH / Chen ZP / Hou WT / Chen YX
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of 2,4-DB-CoA-bound Arabidopsis thaliana fatty acid transporter CTS
Authors: Zha ZH / Chen ZP / Hou WT / Chen YX
History
DepositionAug 23, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65951.png

Downloads & links

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Map

FileDownload / File: emd_65951.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.8061401 - 2.0576117
Average (Standard dev.)-0.00036998585 (±0.034123052)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65951_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65951_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis thaliana fatty acid transporter CTS

EntireName: Arabidopsis thaliana fatty acid transporter CTS
Components
  • Complex: Arabidopsis thaliana fatty acid transporter CTS
    • Protein or peptide: ABC transporter D family member 1
  • Ligand: ~{S}-[2-[3-[[(2~{S})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 4-[2,4-bis(chloranyl)phenoxy]butanethioate
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Arabidopsis thaliana fatty acid transporter CTS

SupramoleculeName: Arabidopsis thaliana fatty acid transporter CTS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: ABC transporter D family member 1

MacromoleculeName: ABC transporter D family member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type fatty-acyl-CoA transporter
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 149.7665 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPSLQLLQLT ERGRGLVASR RKSILLAAGI VAAGGTAVYL KSRVASRRPD SSRLCNGQSD DDETLEKLTA TDQNAKITTK KKKGGGLKS LQVLTAILLS QMGKMGARDL LALVATVVFR TALSNRLAKV QGFLFRAAFL RRAPLFLRLI SENIMLCFML S TLHSTSKY ...String:
MPSLQLLQLT ERGRGLVASR RKSILLAAGI VAAGGTAVYL KSRVASRRPD SSRLCNGQSD DDETLEKLTA TDQNAKITTK KKKGGGLKS LQVLTAILLS QMGKMGARDL LALVATVVFR TALSNRLAKV QGFLFRAAFL RRAPLFLRLI SENIMLCFML S TLHSTSKY ITGALSLRFR KILTKIIHSH YFENMVYYKI SHVDGRITHP EQRIASDVPR FSSELSDLIL DDLTAVTDGI LY AWRLCSY ASPKYIFWIL AYVLGAGTAI RNFSPSFGKL MSKEQQLEGE YRQLHSRLRT HSESIAFYGG ETREESHIQQ KFK NLVSHM SHVLHDHWWF GMIQDFLLKY LGATVAVILI IEPFFSGHLR PDDSTLGRAE MLSNIRYHTS VIISLFQALG TLSI SSRRL NRLSGYADRI HELMAVSREL SGDDKSSFQR NRSRNYLSEA NYVEFSDVKV VTPTGNVLVE DLTLRVEQGS NLLIT GPNG SGKSSLFRVL GGLWPLVSGH IVKPGVGSDL NKEIFYVPQR PYMAVGTLRD QLIYPLTSGQ ESELLTEIGM VELLKN VDL EYLLDRYQPE KEVNWGDELS LGEQQRLGMA RLFYHKPKFA ILDECTSAVT TDMEERFAAK VRAMGTSCIT ISHRPAL VA FHDVVLSLDG EGGWSVHYKR DDSALLTDAE IDSVKSSDTD RQNDAMVVQR AFAAARKESA TNSKAQSYQT QLIARSPV V DKSVVLPRFP QPQTSQRALP SRVAAMLNVL IPTIFDKQGA QLLAVACLVV SRTLISDRIA SLNGTTVKYV LEQDKAAFV RLIGLSVLQS GASSIIAPSL RHLTQRLALG WRIRLTQHLL RNYLRNNAFY KVFHMSGNSI DADQRLTRDL EKLTADLSGL LTGMVKPSV DILWFTWRMK LLTGQRGVAI LYTYMLLGLG FLRRVAPDFG DLAGEEQQLE GKFRFMHERL NTHAESIAFF G GGAREKAM VDKKFRALLD HSLMLLRKKW LYGILDDFVT KQLPNNVTWG LSLLYALEHK GDRALVSTQG ELAHALRYLA SV VSQSFMA FGDILELHKK FLELSGGINR IFELDEFLDA SQSGVTSENQ TSRLDSQDLL SFSEVDIITP AQKLMASKLS CEI VSGKSL LVTGPNGSGK TSVFRVLRDI WPTVCGRLTK PSLDIKELGS GNGMFFVPQR PYTCLGTLRD QIIYPLSKEE AEKR AAKLY TSGESSTEAG SILDSHLKTI LENVRLVYLL ERDVGGWDAT TNWEDILSLG EQQRLGMARL FFHRPKFGVL DECTN ATSV DVEEQLYRVA RDMGVTFITS SQRPALIPFH SLELRLIDGE GNWELRSIEQ TTE

UniProtKB: ABC transporter D family member 1

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Macromolecule #2: ~{S}-[2-[3-[[(2~{S})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopur...

MacromoleculeName: ~{S}-[2-[3-[[(2~{S})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl- ...Name: ~{S}-[2-[3-[[(2~{S})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 4-[2,4-bis(chloranyl)phenoxy]butanethioate
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1EWA
Molecular weightTheoretical: 998.609 Da

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.2 µm / Nominal defocus min: 1.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot (ver. 0.9.8.7) / Number images used: 572683
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

9wfg


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9wg8:
Cryo-EM structure of 2,4-DB-CoA-bound Arabidopsis thaliana fatty acid transporter CTS

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