8DKM

Cryo-EM structure of cystine-bound cystinosin in a lumen-open state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and mechanism of human cystine exporter cystinosin.

Guo, X.Schmiege, P.Assafa, T.E.Wang, R.Xu, Y.Donnelly, L.Fine, M.Ni, X.Jiang, J.Millhauser, G.Feng, L.Li, X.

(2022) Cell 185: 3739-3752.e18

  • DOI: https://doi.org/10.1016/j.cell.2022.08.020
  • Primary Citation of Related Structures:  
    8DKE, 8DKI, 8DKM, 8DKW, 8DKX, 8DYP

  • PubMed 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 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.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 3H5 Heavy Chain250Mus musculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab 3H5 Kappa chain233Mus musculusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of CystinosinC [auth P]408Homo sapiensMutation(s): 1 
Gene Names: CTNS
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O60931 (Homo sapiens)
Explore O60931 
Go to UniProtKB:  O60931
PHAROS:  O60931
GTEx:  ENSG00000040531 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60931
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IYY (Subject of Investigation/LOI)
Query on IYY

Download Ideal Coordinates CCD File 
D [auth P]L-cystine
C6 H12 N2 O4 S2
LEVWYRKDKASIDU-IMJSIDKUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.39 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--
Welch FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2022-10-12
    Changes: Database references