+Open data
-Basic information
Entry | Database: PDB / ID: 8r8q | ||||||
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Title | Lysosomal peptide transporter | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / MFS transporter / MFSD family / nutrition transporter / lysosomal transporter / outward open | ||||||
Function / homology | Function and homology information protein localization to lysosome / transmembrane transporter activity / lysosome / protein stabilization / lysosomal membrane / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.08 Å | ||||||
Authors | Jungnickel, K.E.J. / Loew, C. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Cell Biol / Year: 2024 Title: MFSD1 with its accessory subunit GLMP functions as a general dipeptide uniporter in lysosomes. Authors: Katharina Esther Julia Jungnickel / Océane Guelle / Miharu Iguchi / Wentao Dong / Vadim Kotov / Florian Gabriel / Cécile Debacker / Julien Dairou / Isabelle McCort-Tranchepain / Nouf N ...Authors: Katharina Esther Julia Jungnickel / Océane Guelle / Miharu Iguchi / Wentao Dong / Vadim Kotov / Florian Gabriel / Cécile Debacker / Julien Dairou / Isabelle McCort-Tranchepain / Nouf N Laqtom / Sze Ham Chan / Akika Ejima / Kenji Sato / David Massa López / Paul Saftig / Ahmad Reza Mehdipour / Monther Abu-Remaileh / Bruno Gasnier / Christian Löw / Markus Damme / 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 ...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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r8q.cif.gz | 141.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r8q.ent.gz | 107.8 KB | Display | PDB format |
PDBx/mmJSON format | 8r8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r8q_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8r8q_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8r8q_validation.xml.gz | 32.6 KB | Display | |
Data in CIF | 8r8q_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/8r8q ftp://data.pdbj.org/pub/pdb/validation_reports/r8/8r8q | HTTPS FTP |
-Related structure data
Related structure data | 19006MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 55765.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mfsd1 / Production host: Homo sapiens (human) / References: UniProt: Q9DC37 | ||
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#2: Protein | Mass: 43102.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Glmp / Production host: Homo sapiens (human) / References: UniProt: Q9JHJ3 | ||
#3: Sugar | ChemComp-NAG / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: GLMP-MFSD1 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3.33 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: PROPANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3193 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 400191 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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