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- EMDB-49388: CryoEM structure of human ABCD3 -

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Basic information

Entry
Database: EMDB / ID: EMD-49388
TitleCryoEM structure of human ABCD3
Map dataSharpened map
Sample
  • Complex: ABCD3 dimer
    • Protein or peptide: ATP-binding cassette sub-family D member 3
KeywordsABC transporter / Peroxisome / Fatty-acid transport / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsGupta M / Khandelwal NK / Stroud RM
Funding support United States, 1 items
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, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49388.png

Downloads & links

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Map

FileDownload / File: emd_49388.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.54
Minimum - Maximum-3.6093264 - 5.2316523
Average (Standard dev.)0.008045472 (±0.092935815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 302.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49388_msk_1.map
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Additional map: Unsharpened map

Fileemd_49388_additional_1.map
AnnotationUnsharpened map
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Half map: Half map A

Fileemd_49388_half_map_1.map
AnnotationHalf map A
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Half map: Half map B

Fileemd_49388_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : ABCD3 dimer

EntireName: ABCD3 dimer
Components
  • Complex: ABCD3 dimer
    • Protein or peptide: ATP-binding cassette sub-family D member 3

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Supramolecule #1: ABCD3 dimer

SupramoleculeName: ABCD3 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ATP-binding cassette sub-family D member 3

MacromoleculeName: ATP-binding cassette sub-family D member 3 / type: protein_or_peptide / ID: 1 / Details: ABCD3-thrombin_cleavage_site-GS_linker-8XHis_tag / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Thioester hydrolases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 78.243727 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAFSKYLTA RNSSLAGAAF LLLCLLHKRR RALGLHGKKS GKPPLQNNEK EGKKERAVVD KVFFSRLIQI LKIMVPRTFC KETGYLVLI AVMLVSRTYC DVWMIQNGTL IESGIIGRSR KDFKRYLLNF IAAMPLISLV NNFLKYGLNE LKLCFRVRLT K YLYEEYLQ ...String:
MAAFSKYLTA RNSSLAGAAF LLLCLLHKRR RALGLHGKKS GKPPLQNNEK EGKKERAVVD KVFFSRLIQI LKIMVPRTFC KETGYLVLI AVMLVSRTYC DVWMIQNGTL IESGIIGRSR KDFKRYLLNF IAAMPLISLV NNFLKYGLNE LKLCFRVRLT K YLYEEYLQ AFTYYKMGNL DNRIANPDQL LTQDVEKFCN SVVDLYSNLS KPFLDIVLYI FKLTSAIGAQ GPASMMAYLV VS GLFLTRL RRPIGKMTIT EQKYEGEYRY VNSRLITNSE EIAFYNGNKR EKQTVHSVFR KLVEHLHNFI LFRFSMGFID SII AKYLAT VVGYLVVSRP FLDLSHPRHL KSTHSELLED YYQSGRMLLR MSQALGRIVL AGREMTRLAG FTARITELMQ VLKD LNHGK YERTMVSQQE KGIEGVQVIP LIPGAGEIII ADNIIKFDHV PLATPNGDVL IRDLNFEVRS GANVLICGPN GCGKS SLFR VLGELWPLFG GRLTKPERGK LFYVPQRPYM TLGTLRDQVI YPDGREDQKR KGISDLVLKE YLDNVQLGHI LEREGG WDS VQDWMDVLSG GEKQRMAMAR LFYHKPQFAI LDECTSAVSV DVEGYIYSHC RKVGITLFTV SHRKSLWKHH EYYLHMD GR GNYEFKQITE DTVEFGSGSG LVPRGSGGGG SGGGGSGGHH HHHHHH

UniProtKB: ATP-binding cassette sub-family D member 3

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 0.002 µm / Nominal defocus min: 0.001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 132775
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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