24VC | pdb_000024vc

Structure of lumen-open ABCD4-LMBD1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation

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This is version 1.0 of the entry. See complete history

Literature

Structural basis for LMBD1-dependent trafficking and cobalamin export of ABCD4.

Liu, Q.Li, X.Wu, Y.Zheng, K.Zhou, M.Long, T.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-026-74552-5
  • Primary Citation Related Structures: 
    24VC, 24VD, 24VE

  • PubMed Abstract: 

    Correct trafficking of lysosomal transporters is essential for intracellular homeostasis. While most lysosomal membrane proteins are directed to the lysosome via sorting motifs, the cobalamin exporter ABCD4 is distinct, instead relying on LMBD1 as a dedicated chaperone for its trafficking. Dysfunction of either protein causes inherited cobalamin metabolism disorders. Despite its physiological significance, the molecular mechanism underlying this chaperone-dependent trafficking remains unclear. Here, we report the cryo-EM structures of ABCD4 complex with LMBD1 in the lumen-open, substrate-bound and cytosol-open states. LMBD1 contains nine transmembrane-helices (TMs) and a cytosolic domain, both of which engage ABCD4. Cell imaging shows that disruption of these interactions impairs the trafficking of ABCD4 to lysosomes. Structural and biochemical analyses provide insights into cobalamin recognition and reveal conformational states associated with the proposed cobalamin transport cycle. These findings provide molecular insights into cobalamin metabolism and illustrate a chaperone-assisted mechanism that supports proper trafficking of a lysosomal transporter.


  • Organizational Affiliation
    • State Key Laboratory of Metabolism and Regulation in Complex Organisms, Taikang Medical School (School of Basic Medical Sciences), Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.

Macromolecule Content 

  • Total Structure Weight: 200.27 kDa 
  • Atom Count: 12,715 
  • Modeled Residue Count: 1,561 
  • Deposited Residue Count: 1,752 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysosomal cobalamin transporter ABCD4
A, B
606Homo sapiensMutation(s): 3 
Gene Names: ABCD4PXMP1L
EC: 7.6.2.8
UniProt & NIH Common Fund Data Resources
Find proteins for O14678 (Homo sapiens)
Explore O14678 
Go to UniProtKB:  O14678
PHAROS:  O14678
GTEx:  ENSG00000119688 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14678
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysosomal cobalamin transport escort protein LMBD1540Homo sapiensMutation(s): 1 
Gene Names: LMBRD1C6orf209NESIBM-021CD001MSTP044
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUN5 (Homo sapiens)
Explore Q9NUN5 
Go to UniProtKB:  Q9NUN5
PHAROS:  Q9NUN5
GTEx:  ENSG00000168216 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NUN5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

Currently 24VC does not have a validation slider image.



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release