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- PDB-9ngj: CryoEM structure of human ABCD3 bound to Phytanoyl-CoA -

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Basic information

Entry
Database: PDB / ID: 9ngj
TitleCryoEM structure of human ABCD3 bound to Phytanoyl-CoA
ComponentsATP-binding cassette sub-family D member 3
KeywordsTRANSPORT PROTEIN / ABC transporter / Peroxisome / Fatty-acid transport
Function / homology
Function and homology information


phytanic acid metabolic process / very long-chain fatty acid metabolic process / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / Class I peroxisomal membrane protein import / fatty acyl-CoA hydrolase activity / peroxisome organization / ABC transporters in lipid homeostasis / bile acid biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases ...phytanic acid metabolic process / very long-chain fatty acid metabolic process / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / Class I peroxisomal membrane protein import / fatty acyl-CoA hydrolase activity / peroxisome organization / ABC transporters in lipid homeostasis / bile acid biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / peroxisomal membrane / long-chain fatty acid transmembrane transporter activity / fatty acid beta-oxidation / bile acid and bile salt transport / RHOC GTPase cycle / peroxisomal matrix / RHOA GTPase cycle / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / fatty acid biosynthetic process / peroxisome / response to xenobiotic stimulus / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding / membrane / cytosol
Similarity search - Function
Peroxysomal long chain fatty acyl transporter / 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 ...Peroxysomal long chain fatty acyl transporter / 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
: / ATP-binding cassette sub-family D member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsGupta, M. / Khandelwal, N.K. / Stroud, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Molecular mechanism of substrate transport by human peroxisomal ABCD3.
Authors: Meghna Gupta / Nitesh Kumar Khandelwal / Devin J Seka / Sree Ganesh Balasubramani / Miles Sasha Dickinson / Alexander Myasnikov / Ignacia Echeverria / Robert M Stroud /
Abstract: ATP-binding cassette transporters of the D subfamily (ABCD1-3) mediate the export of CoA thioesters of fatty acids from the cytosol into peroxisomes for further oxidation. ABCD3 facilitates the ...ATP-binding cassette transporters of the D subfamily (ABCD1-3) mediate the export of CoA thioesters of fatty acids from the cytosol into peroxisomes for further oxidation. ABCD3 facilitates the transport of a broad spectrum of substrates, including branched-chain fatty acids, very long-chain fatty acids, bile salt intermediates, and dicarboxylic acids as CoA adducts. Mutations in ABCD3 are associated with defects in congenital bile acid synthesis. Despite its importance, the basis for substrate selectivity and the mechanism of transport by ABCD3 are not well defined. We report the cryogenic sample electron microscopy (cryo-EM) structures of full-length human ABCD3 in its apo state and bound to one of its physiological substrates (phytanoyl-CoA) at resolutions of 3.33 Å and 3.13 Å, respectively. Our biochemical assays reveal that substrate binding induces ATPase activity in ABCD3, suggesting a substrate-dependent conformational change. Structural comparison of the apo and substrate-bound states demonstrates that the substrate interaction brings nucleotide-binding domains closer together, providing a mechanistic basis of substrate-induced ATPase activity. These findings offer critical insights into the transport mechanism of ABCD3 and lay a structural foundation for understanding its role in peroxisomal metabolite import and related diseases.
History
DepositionFeb 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ATP-binding cassette sub-family D member 3
A: ATP-binding cassette sub-family D member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,6124
Polymers156,4872
Non-polymers2,1242
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ATP-binding cassette sub-family D member 3 / 70 kDa peroxisomal membrane protein / PMP70


Mass: 78243.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ABCD3-thrombin_cleavage_site-GS_linker-8XHis_tag / Source: (gene. exp.) Homo sapiens (human) / Gene: ABCD3, PMP70, PXMP1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P28288, Hydrolases; Acting on ester bonds; Thioester hydrolases, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#2: Chemical ChemComp-A1CAN / S-{(3R,5S,9S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (3S,7R,11R)-3,7,11,15-tetramethylhexadecanethioate (non-preferred name)


Mass: 1062.049 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H74N7O17P3S / 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: ABCD3 dimer with Phytanoyl-CoA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 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: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2 nm / Nominal defocus min: 1 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 2 sec. / Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1
Image scansSampling size: 5 µm

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21_5207model refinement
3SerialEMimage acquisition
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 283849 / Symmetry type: POINT
RefinementHighest resolution: 3.13 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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