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- PDB-9wg2: Cryo-EM structure of IBA-CoA-bound Arabidopsis thaliana fatty aci... -

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Basic information

Entry
Database: PDB / ID: 9wg2
TitleCryo-EM structure of IBA-CoA-bound Arabidopsis thaliana fatty acid transporter CTS
ComponentsABC transporter D family member 1
KeywordsMEMBRANE PROTEIN / ABC transporter / fatty acid transporter
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
: / CHOLESTEROL HEMISUCCINATE / ABC transporter D family member 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZha, Z.H. / Chen, Z.P. / Hou, W.T. / Chen, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of IBA-CoA-bound Arabidopsis thaliana fatty acid transporter CTS
Authors: Zha, Z.H. / Chen, Z.P. / Hou, W.T. / Chen, Y.X.
History
DepositionAug 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 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 D family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,2063
Polymers149,7671
Non-polymers1,4392
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 D family member 1 / ABC transporter ABCD.1 / AtABCD1 / Peroxisomal ABC transporter 1 / AtPXA1 / Protein ACETATE NON- ...ABC transporter ABCD.1 / AtABCD1 / Peroxisomal ABC transporter 1 / AtPXA1 / Protein ACETATE NON-UTILIZING 2 / Protein COMATOSE / Protein PEROXISOME DEFECTIVE 3 / Ped3p


Mass: 149766.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: ABCD1, ACN2, CTS, PED3, PMP2, PXA1, At4g39850, T5J17.20
Production host: Homo sapiens (human)
References: UniProt: Q94FB9, ABC-type fatty-acyl-CoA transporter
#2: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1EV8 / ~{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-(1~{H}-indol-3-yl)butanethioate


Mass: 952.756 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H47N8O17P3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Arabidopsis thaliana fatty acid transporter CTS / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3particle selection
12Coot0.9.8.73D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 353872 / Symmetry type: POINT
Atomic model buildingPDB-ID: 9WFG

9wfg


Accession code: 9WFG / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039707
ELECTRON MICROSCOPYf_angle_d0.62113140
ELECTRON MICROSCOPYf_dihedral_angle_d9.2841339
ELECTRON MICROSCOPYf_chiral_restr0.041498
ELECTRON MICROSCOPYf_plane_restr0.0031654

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