6L85 | pdb_00006l85

The sodium-dependent phosphate transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6L85

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 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.).

Macromolecule Content 

  • Total Structure Weight: 88.48 kDa 
  • Atom Count: 6,300 
  • Modeled Residue Count: 801 
  • Deposited Residue Count: 804 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
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

View Full Validation Report



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