8Z0F | pdb_00008z0f

Cryo-EM structure of ATP-bound human very long-chain fatty acid ABC transporter ABCD3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into human ABCD3-mediated peroxisomal acyl-CoA translocation.

Li, Y.Chen, Z.P.Xu, D.Wang, L.Cheng, M.T.Zhou, C.Z.Chen, Y.Hou, W.T.

(2024) Cell Discov 10: 92-92

  • DOI: https://doi.org/10.1038/s41421-024-00722-8
  • Primary Citation of Related Structures:  
    8Z0F, 8Z9X

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-binding cassette sub-family D member 3
A, B
668Homo sapiensMutation(s): 1 
Gene Names: ABCD3PMP70PXMP1
EC: 3.1.2 (PDB Primary Data), 7.6.2 (PDB Primary Data)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P28288 (Homo sapiens)
Explore P28288 
Go to UniProtKB:  P28288
PHAROS:  P28288
GTEx:  ENSG00000117528 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28288
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32071206

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2025-04-23
    Changes: Data collection, Database references, Structure summary