8R8Q | pdb_00008r8q

Lysosomal peptide transporter

• PDB DOI: https://doi.org/10.2210/pdb8R8Q/pdb
• EM Map EMD-19006: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2023-11-29 Released: 2024-05-01 
• Deposition Author(s): Jungnickel, K.E.J., Loew, C.
• Funding Organization(s): Other government

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Experimental Data Snapshot

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

Starting Model: in silico

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 26: 1047-1061

• PubMed: 38839979 
• DOI: https://doi.org/10.1038/s41556-024-01436-5
• Primary Citation 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.

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Organizational Affiliation: 
• Centre for Structural Systems Biology, Hamburg, Germany.
European Molecular Biology Laboratory Hamburg, Hamburg, Germany.
Saints-Pères Paris Institute for the Neurosciences, Université Paris Cité, Centre National de la Recherche Scientifique, Paris, France.
Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
Department of Genetics, Stanford University, Stanford, CA, USA.
The Institute for Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, USA.
Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Cité, Paris, France.
Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, USA.
Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany.
UGent Center for Molecular Modeling, Ghent University, Ghent, Belgium.
Saints-Pères Paris Institute for the Neurosciences, Université Paris Cité, Centre National de la Recherche Scientifique, Paris, France. [e-mail].
Centre for Structural Systems Biology, Hamburg, Germany. [e-mail].
European Molecular Biology Laboratory Hamburg, Hamburg, Germany. [e-mail].
Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 99.97 kDa 
• Atom Count: 5,702 
• Modeled Residue Count: 732 
• Deposited Residue Count: 909 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major facilitator superfamily domain-containing protein 1	A	506	Mus musculus	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosylated lysosomal membrane protein	B	403	Mus musculus	Mutation(s): 0  Gene Names: Glmp Membrane Entity: Yes
UniProt
Find proteins for Q9JHJ3 (Mus musculus) Explore Q9JHJ3  Go to UniProtKB:  Q9JHJ3
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: Q9JHJ3-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth B], D [auth B], E [auth B], F [auth B], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1-4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Jungnickel, K.E.J., Loew, C.

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Funding Organization	Location	Grant Number
Other government	Germany	05K18YEA

Revision History  

• 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
• Version 1.3: 2024-07-24
  Changes: Data collection, Database references
• Version 1.4: 2024-11-06
  Changes: Data collection, Structure summary