6L85

The sodium-dependent phosphate transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure of the sodium-dependent phosphate transporter reveals insights into human solute carrier SLC20.

Tsai, J.-Y.Chu, C.-H.Lin, M.-G.Chou, Y.-H.Hong, R.-Y.Yen, C.-Y.Hsiao, C.-D.Sun, Y.-J.

(2020) Sci Adv 6: eabb4024-eabb4024

  • DOI: https://doi.org/10.1126/sciadv.abb4024
  • Primary Citation of Related Structures:  
    6L85

  • PubMed Abstract: 

    Inorganic phosphate (P i ) is a fundamental and essential element for nucleotide biosynthesis, energy supply, and cellular signaling in living organisms. Human phosphate transporter ( h PiT) dysfunction causes numerous diseases, but the molecular mechanism underlying transporters remains elusive. We report the structure of the sodium-dependent phosphate transporter from Thermotoga maritima ( Tm PiT) in complex with sodium and phosphate ( Tm PiT-Na/Pi) at 2.3-angstrom resolution. We reveal that one phosphate and two sodium ions (Pi-2Na) are located at the core of Tm PiT and that the third sodium ion (Na fore ) is located near the inner membrane boundary. We propose an elevator-like mechanism for sodium and phosphate transport by Tm PiT, with the Tm PiT-Na/Pi complex adopting an inward occluded conformation. We found that disease-related h PiT variants carry mutations in the corresponding sodium- and phosphate-binding residues identified in Tm PiT. Our three-dimensional structure of Tm PiT provides a framework for understanding PiT dysfunction and for future structure-based drug design.


  • Organizational Affiliation

    Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan (R.O.C.).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphate transporter
A, B
402Thermotoga maritima MSB8Mutation(s): 0 
Gene Names: Tmari_0259
Membrane Entity: Yes 
UniProt
Find proteins for Q9WY99 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WY99 
Go to UniProtKB:  Q9WY99
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WY99
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
N [auth A],
O [auth A],
X [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
P [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
Q [auth B]
R [auth B]
D [auth A],
E [auth A],
F [auth A],
Q [auth B],
R [auth B],
S [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.178α = 90
b = 112.65β = 119.36
c = 110.792γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (Taiwan)Taiwan108-2321-B-007-002
Ministry of Science and Technology (Taiwan)Taiwan108-2811-B-007-504

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references