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- EMDB-39871: Cryo-EM structure of Phytanoyl-CoA-bound human very long-chain fa... -

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Basic information

Entry
Database: EMDB / ID: EMD-39871
TitleCryo-EM structure of Phytanoyl-CoA-bound human very long-chain fatty acid ABC transporter ABCD3
Map data
Sample
  • Complex: Phytanoyl-CoA-bound human peroxisomal ABCD3
    • Protein or peptide: ATP-binding cassette sub-family D member 3
  • Ligand: phytanoyl-CoA
Keywordsvery long-chain fatty / Peroxisome / ABC transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


phytanic acid metabolic process / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / very long-chain fatty acid metabolic process / Class I peroxisomal membrane protein import / peroxisome organization / fatty acyl-CoA hydrolase activity / ABC transporters in lipid homeostasis / bile acid biosynthetic process / Hydrolases; Acting on ester bonds; Thioester hydrolases ...phytanic acid metabolic process / long-chain fatty acid import into peroxisome / very long-chain fatty acid catabolic process / very long-chain fatty acid metabolic process / Class I peroxisomal membrane protein import / peroxisome organization / fatty acyl-CoA hydrolase activity / 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 / bile acid and bile salt transport / fatty acid beta-oxidation / 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 / intracellular membrane-bounded organelle / 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: 2.96 Å
AuthorsLi Y / Chen YX / Zhou CZ / Hou WT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071206 China
CitationJournal: Cell Discov / Year: 2024
Title: Structural insights into human ABCD3-mediated peroxisomal acyl-CoA translocation.
Authors: Yang Li / Zhi-Peng Chen / Da Xu / Liang Wang / Meng-Ting Cheng / Cong-Zhao Zhou / Yuxing Chen / Wen-Tao Hou /
Abstract: Human ABC transporters ABCD1-3 are all localized on the peroxisomal membrane and participate in the β-oxidation of fatty acyl-CoAs, but they differ from each other in substrate specificity. The ...Human ABC transporters ABCD1-3 are all localized on the peroxisomal membrane and participate in the β-oxidation of fatty acyl-CoAs, but they differ from each other in substrate specificity. The transport of branched-chain fatty acids from cytosol to peroxisome is specifically driven by ABCD3, dysfunction of which causes severe liver diseases such as hepatosplenomegaly. Here we report two cryogenic electron microscopy (cryo-EM) structures of ABCD3 bound to phytanoyl-CoA and ATP at resolutions of 2.9 Å and 3.2 Å, respectively. A pair of phytanoyl-CoA molecules were observed in ABCD3, each binding to one transmembrane domain (TMD), which is distinct from our previously reported structure of ABCD1, where each fatty acyl-CoA molecule strongly crosslinks two TMDs. Upon ATP binding, ABCD3 exhibits a conformation that is open towards the peroxisomal matrix, leaving two extra densities corresponding to two CoA molecules deeply embedded in the translocation cavity. Structural analysis combined with substrate-stimulated ATPase activity assays indicated that the present structures might represent two states of ABCD3 in the transport cycle. These findings advance our understanding of fatty acid oxidation and the molecular pathology of related diseases.
History
DepositionApr 23, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39871.png

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Map

FileDownload / File: emd_39871.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.371
Minimum - Maximum-1.5638444 - 2.5394604
Average (Standard dev.)-0.00027920963 (±0.05299105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_39871_additional_1.map
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Half map: #2

Fileemd_39871_half_map_1.map
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Half map: #1

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Sample components

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Entire : Phytanoyl-CoA-bound human peroxisomal ABCD3

EntireName: Phytanoyl-CoA-bound human peroxisomal ABCD3
Components
  • Complex: Phytanoyl-CoA-bound human peroxisomal ABCD3
    • Protein or peptide: ATP-binding cassette sub-family D member 3
  • Ligand: phytanoyl-CoA

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Supramolecule #1: Phytanoyl-CoA-bound human peroxisomal ABCD3

SupramoleculeName: Phytanoyl-CoA-bound human peroxisomal ABCD3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 140 kDa/nm

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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 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Thioester hydrolases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.67918 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKA VFSKLQLLGQ AIPPKQYAPG VVGMLAVFAL IKLYKQDIRG TKHLVAKTKE GKKERAVVDK VFFSRLIQIL KIMVPRTFC KETGYLVLIA VMLVSRTYCD VWMIQNGTLI ESGIIGRSRK DFKRYLLNFI AAMPLISLVN NFLKYGLNEL K LCFRVRLT ...String:
MDYKDDDDKA VFSKLQLLGQ AIPPKQYAPG VVGMLAVFAL IKLYKQDIRG TKHLVAKTKE GKKERAVVDK VFFSRLIQIL KIMVPRTFC KETGYLVLIA VMLVSRTYCD VWMIQNGTLI ESGIIGRSRK DFKRYLLNFI AAMPLISLVN NFLKYGLNEL K LCFRVRLT KYLYEEYLQA FTYYKMGNLD NRIANPDQLL TQDVEKFCNS VVDLYSNLSK PFLDIVLYIF KLTSAIGAQG PA SMMAYLV VSGLFLTRLR RPIGKMTITE QKYEGEYRYV NSRLITNSEE IAFYNGNKRE KQTVHSVFRK LVEHLHNFIL FRF SMGFID SIIAKYLATV VGYLVVSRPF LDLSHPRHLK STHSELLEDY YQSGRMLLRM SQALGRIVLA GREMTRLAGF TARI TELMQ VLKDLNHGKY ERTMVSQQEK GIEGVQVIPL IPGAGEIIIA DNIIKFDHVP LATPNGDVLI RDLNFEVRSG ANVLI CGPN GCGKSSLFRV LGELWPLFGG RLTKPERGKL FYVPQRPYMT LGTLRDQVIY PDGREDQKRK GISDLVLKEY LDNVQL GHI LEREGGWDSV QDWMDVLSGG EKQRMAMARL FYHKPQFAIL DECTSAVSVD VEGYIYSHCR KVGITLFTVS HRKSLWK HH EYYLHMDGRG NYEFKQITED TVEFGS

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

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Macromolecule #2: phytanoyl-CoA

MacromoleculeName: phytanoyl-CoA / type: ligand / ID: 2 / Number of copies: 2 / Formula: A1L1A
Molecular weightTheoretical: 1.062049 KDa

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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

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96695
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5

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