8R8Q

Lysosomal peptide transporter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

MFSD1 with its accessory subunit GLMP functions as a general dipeptide uniporter in lysosomes.

Jungnickel, K.E.J.Guelle, O.Iguchi, M.Dong, W.Kotov, V.Gabriel, F.Debacker, C.Dairou, J.McCort-Tranchepain, I.Laqtom, N.N.Chan, S.H.Ejima, A.Sato, K.Massa Lopez, D.Saftig, P.Mehdipour, A.R.Abu-Remaileh, M.Gasnier, B.Low, C.Damme, M.

(2024) Nat Cell Biol 

  • DOI: https://doi.org/10.1038/s41556-024-01436-5
  • Primary Citation of Related Structures:  
    8R8Q

  • PubMed Abstract: 

    The lysosomal degradation of macromolecules produces diverse small metabolites exported by specific transporters for reuse in biosynthetic pathways. Here we deorphanized the major facilitator superfamily domain containing 1 (MFSD1) protein, which forms a tight complex with the glycosylated lysosomal membrane protein (GLMP) in the lysosomal membrane. Untargeted metabolomics analysis of MFSD1-deficient mouse lysosomes revealed an increase in cationic dipeptides. Purified MFSD1 selectively bound diverse dipeptides, while electrophysiological, isotope tracer and fluorescence-based studies in Xenopus oocytes and proteoliposomes showed that MFSD1-GLMP acts as a uniporter for cationic, neutral and anionic dipeptides. Cryoelectron microscopy structure of the dipeptide-bound MFSD1-GLMP complex in outward-open conformation characterized the heterodimer interface and, in combination with molecular dynamics simulations, provided a structural basis for its selectivity towards diverse dipeptides. Together, our data identify MFSD1 as a general lysosomal dipeptide uniporter, providing an alternative route to recycle lysosomal proteolysis products when lysosomal amino acid exporters are overloaded.


  • Organizational Affiliation

    Centre for Structural Systems Biology, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major facilitator superfamily domain-containing protein 1506Mus musculusMutation(s): 0 
Gene Names: Mfsd1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9DC37 (Mus musculus)
Explore Q9DC37 
Go to UniProtKB:  Q9DC37
IMPC:  MGI:1914118
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9DC37
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosylated lysosomal membrane protein403Mus musculusMutation(s): 0 
Gene Names: Glmp
Membrane Entity: Yes 
UniProt
Find proteins for Q9JHJ3 (Mus musculus)
Explore Q9JHJ3 
Go to UniProtKB:  Q9JHJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JHJ3
Glycosylation
Glycosylation Sites: 5Go to GlyGen: Q9JHJ3-1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGermany05K18YEA

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Database references