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- PDB-8dkm: Cryo-EM structure of cystine-bound cystinosin in a lumen-open state -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dkm | |||||||||
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Title | Cryo-EM structure of cystine-bound cystinosin in a lumen-open state | |||||||||
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![]() | MEMBRANE PROTEIN/Transport protein / Cystine / transporter / lysosome / MEMBRANE PROTEIN / MEMBRANE PROTEIN-Transport protein complex | |||||||||
Function / homology | ![]() proximal tubule morphogenesis / regulation of melanin biosynthetic process / solute:proton symporter activity / L-cystine transmembrane transporter activity / positive regulation of thyroid hormone generation / brush border assembly / renal water absorption / L-cystine transport / renal phosphate ion absorption / renal glucose absorption ...proximal tubule morphogenesis / regulation of melanin biosynthetic process / solute:proton symporter activity / L-cystine transmembrane transporter activity / positive regulation of thyroid hormone generation / brush border assembly / renal water absorption / L-cystine transport / renal phosphate ion absorption / renal glucose absorption / Transport of inorganic cations/anions and amino acids/oligopeptides / negative regulation of hydrogen peroxide biosynthetic process / Miscellaneous transport and binding events / regulation of TORC1 signaling / grooming behavior / melanin biosynthetic process / renal albumin absorption / melanosome membrane / amino acid metabolic process / adult walking behavior / positive regulation of mitochondrial membrane potential / lens development in camera-type eye / thyroid gland development / long-term memory / monoatomic ion transport / ATP metabolic process / positive regulation of TORC1 signaling / glutathione metabolic process / visual learning / brain development / transmembrane transport / cognition / melanosome / protein transport / late endosome / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / negative regulation of apoptotic process / extracellular exosome / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å | |||||||||
![]() | Schmiege, P. / Li, X. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and mechanism of human cystine exporter cystinosin. Authors: Xue Guo / Philip Schmiege / Tufa E Assafa / Rong Wang / Yan Xu / Linda Donnelly / Michael Fine / Xiaodan Ni / Jiansen Jiang / Glenn Millhauser / Liang Feng / Xiaochun Li / ![]() Abstract: Lysosomal amino acid efflux by proton-driven transporters is essential for lysosomal homeostasis, amino acid recycling, mTOR signaling, and maintaining lysosomal pH. To unravel the mechanisms of ...Lysosomal amino acid efflux by proton-driven transporters is essential for lysosomal homeostasis, amino acid recycling, mTOR signaling, and maintaining lysosomal pH. To unravel the mechanisms of these transporters, we focus on cystinosin, a prototypical lysosomal amino acid transporter that exports cystine to the cytosol, where its reduction to cysteine supplies this limiting amino acid for diverse fundamental processes and controlling nutrient adaptation. Cystinosin mutations cause cystinosis, a devastating lysosomal storage disease. Here, we present structures of human cystinosin in lumen-open, cytosol-open, and cystine-bound states, which uncover the cystine recognition mechanism and capture the key conformational states of the transport cycle. Our structures, along with functional studies and double electron-electron resonance spectroscopic investigations, reveal the molecular basis for the transporter's conformational transitions and protonation switch, show conformation-dependent Ragulator-Rag complex engagement, and demonstrate an unexpected activation mechanism. These findings provide molecular insights into lysosomal amino acid efflux and a potential therapeutic strategy. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.7 KB | Display | ![]() |
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PDB format | ![]() | 84 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 27490MC ![]() 8dkeC ![]() 8dkiC ![]() 8dkwC ![]() 8dkxC ![]() 8dypC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Antibody | Mass: 26768.107 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 25468.404 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 46080.355 Da / Num. of mol.: 1 / Mutation: T260I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Chemical | ChemComp-IYY / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 61.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 589358 / Symmetry type: POINT |