[English] 日本語
Yorodumi
- PDB-8dyp: Crystal structure of human cystine transporter cystinosin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dyp
TitleCrystal structure of human cystine transporter cystinosin
Components
  • Cystinosin
  • Nanobody P10
KeywordsTRANSPORT PROTEIN / Lysosomal transporter / Proton-coupled transporter / Cystine transporter / Cystinosis
Function / homology
Function and homology information


regulation of melanin biosynthetic process / solute:proton symporter activity / L-cystine transmembrane transporter activity / L-cystine transport / : / Miscellaneous transport and binding events / regulation of TORC1 signaling / melanin biosynthetic process / grooming behavior / melanosome membrane ...regulation of melanin biosynthetic process / solute:proton symporter activity / L-cystine transmembrane transporter activity / L-cystine transport / : / Miscellaneous transport and binding events / regulation of TORC1 signaling / melanin biosynthetic process / grooming behavior / melanosome membrane / amino acid metabolic process / lens development in camera-type eye / adult walking behavior / long-term memory / ATP metabolic process / monoatomic ion transport / glutathione metabolic process / positive regulation of TORC1 signaling / brain development / visual learning / transmembrane transport / cognition / melanosome / late endosome / protein transport / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / extracellular exosome / plasma membrane
Similarity search - Function
Lysosomal cystine transporter / Repeated motif present between transmembrane helices in cystinosin, yeast ERS1p, mannose-P-dolichol utilization defect 1, and other hypothetical proteins. / PQ-loop repeat / PQ loop repeat / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Cystinosin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsGuo, X. / Feng, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Cell / Year: 2022
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
DepositionAug 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cystinosin
B: Nanobody P10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7415
Polymers50,1932
Non-polymers5493
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.510, 71.270, 194.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

#1: Protein Cystinosin


Mass: 37173.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNS / Production host: Homo sapiens (human) / References: UniProt: O60931
#2: Antibody Nanobody P10


Mass: 13019.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 6.5 / Details: 12% PEG400, 80mM Li2SO4, and 50mM MES pH6.0 / PH range: 6.0-6.8

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B10.9794
SYNCHROTRONAPS 24-ID-E20.9794
SYNCHROTRONAPS 23-ID-B30.9794
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELAug 19, 2018
DECTRIS EIGER X 16M2PIXELJul 21, 2018
DECTRIS EIGER X 16M3PIXELJul 3, 2021
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
21
31
ReflectionResolution: 3.4→40.19 Å / Num. obs: 9815 / % possible obs: 97.3 % / Redundancy: 14.9 % / Biso Wilson estimate: 105.72 Å2 / CC1/2: 0.967 / CC star: 0.992 / Net I/σ(I): 15.2
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.69 / Num. unique obs: 886 / CC1/2: 0.722 / % possible all: 88.9

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
PHENIX1.19.2_4158refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P0G, 4x5n

3p0g

4x5n


Resolution: 3.4→40.19 Å / SU ML: 0.4795 / Cross valid method: FREE R-VALUE / Phase error: 34.0292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.302 975 9.97 %
Rwork0.2704 8804 -
obs0.2721 9779 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.5 Å2
Refinement stepCycle: LAST / Resolution: 3.4→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 35 0 3371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343460
X-RAY DIFFRACTIONf_angle_d0.72354720
X-RAY DIFFRACTIONf_chiral_restr0.0475543
X-RAY DIFFRACTIONf_plane_restr0.0058581
X-RAY DIFFRACTIONf_dihedral_angle_d14.92781167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.580.41181260.33241143X-RAY DIFFRACTION90
3.58-3.80.39891300.32891170X-RAY DIFFRACTION92.72
3.8-4.10.32631390.28651252X-RAY DIFFRACTION99.71
4.1-4.510.27711410.25211277X-RAY DIFFRACTION99.79
4.51-5.160.251400.23921270X-RAY DIFFRACTION99.3
5.16-6.50.31471450.28961309X-RAY DIFFRACTION100
6.5-40.190.28751540.25621383X-RAY DIFFRACTION99.61

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more