[English] 日本語
![](img/lk-miru.gif)
- EMDB-27493: Cryo-EM structure of cystinosin N288K mutant in a cytosol-open st... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of cystinosin N288K mutant in a cytosol-open state at pH7.5 | |||||||||
![]() | Cystinosin N288K mutant at pH7.5 | |||||||||
![]() |
| |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Schmiege P / Li X | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 97 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 17.5 KB 17.5 KB | Display Display | ![]() |
Images | ![]() | 80.8 KB | ||
Others | ![]() ![]() | 95.6 MB 95.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dkxMC ![]() 8dkeC ![]() 8dkiC ![]() 8dkmC ![]() 8dkwC ![]() 8dypC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Cystinosin N288K mutant at pH7.5 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: Half Map 1
File | emd_27493_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half Map 2
File | emd_27493_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Cystinosin N288K - Fab 3H5 complex at pH7.5
Entire | Name: Cystinosin N288K - Fab 3H5 complex at pH7.5 |
---|---|
Components |
|
-Supramolecule #1: Cystinosin N288K - Fab 3H5 complex at pH7.5
Supramolecule | Name: Cystinosin N288K - Fab 3H5 complex at pH7.5 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
---|
-Supramolecule #2: Cystinosin N288K
Supramolecule | Name: Cystinosin N288K / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #3 |
---|---|
Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #3: Fab 3H5
Supramolecule | Name: Fab 3H5 / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #1-#2 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Fab 3H5 Heavy Chain
Macromolecule | Name: Fab 3H5 Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 26.768107 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MGWSCIILFL VATATGVHSE VMLVESGGGL VKPGGSLKLS CAASGFTFSN YAMSWVRQTP EKRLEWVAAI SGNEGTYTYY PDSVRGRFT ISRDNARNNL YLQISSLRSE DTALYYCARY GLVGALDFWG QGASVTVSSA STKGPSVFPL APSSKSTSGG T AALGCLVK ...String: MGWSCIILFL VATATGVHSE VMLVESGGGL VKPGGSLKLS CAASGFTFSN YAMSWVRQTP EKRLEWVAAI SGNEGTYTYY PDSVRGRFT ISRDNARNNL YLQISSLRSE DTALYYCARY GLVGALDFWG QGASVTVSSA STKGPSVFPL APSSKSTSGG T AALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KS CDKTHHH HHH |
-Macromolecule #2: Fab 3H5 Kappa Chain
Macromolecule | Name: Fab 3H5 Kappa Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 25.468404 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MGWSCIILFL VATATGVHSD IQMNQSPSTL SASLGDTITI TCRASQNIDV WLNWYQQKPG DIPKLLIYEA SNLHTGVPSR FSGSGSGTD FTLAISSLQP EDIATYYCLQ GQDYPFTFGS GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK ...String: MGWSCIILFL VATATGVHSD IQMNQSPSTL SASLGDTITI TCRASQNIDV WLNWYQQKPG DIPKLLIYEA SNLHTGVPSR FSGSGSGTD FTLAISSLQP EDIATYYCLQ GQDYPFTFGS GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY P REAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC |
-Macromolecule #3: Isoform 2 of Cystinosin
Macromolecule | Name: Isoform 2 of Cystinosin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 46.095434 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NVSLTLRPPL NATLVITFEI TFRSKNITIL ELPDEVVVPP GVTNSSFQV TSQNVGQLTV YLHGNHSNQT GPRIRFLVIR SSAISIINQV IGWIYFVAWS ISFYPQVIMN WRRKSVIGLS F DFVALNLT ...String: MIRNWLTIFI LFPLKLVEKC ESSVSLTVPP VVKLENGSST NVSLTLRPPL NATLVITFEI TFRSKNITIL ELPDEVVVPP GVTNSSFQV TSQNVGQLTV YLHGNHSNQT GPRIRFLVIR SSAISIINQV IGWIYFVAWS ISFYPQVIMN WRRKSVIGLS F DFVALNLT GFVAYSVFNI GLLWVPYIKE QFLLKYPNGV NPVNSNDVFF SLHAVVLTLI IIVQCCLYER GGQRVSWPAI GF LVLAWLF AFVTMIVAAV GVITWLQFLF CFSYIKLAVT LVKYFPQAYM KFYYKSTEGW SIGNVLLDFT GGSFSLLQMF LQS YNNDQW TLIFGDPTKF GLGVFSIVFD VVFFIQHFCL YRKRPGLQAA RTGSGSRLRQ DWAPSLQPKA LPQTTSVSAS SLKG DYKDD DDK |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 61.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 323738 |
---|---|
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |