9RXT | pdb_00009rxt

Structure of the PDZ1 domain from human NHERF1 with the C-terminal residues (NATRL) of the human sodium-dependent phosphate transporter 2A (NaPi-IIa, SLC34A1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free: 
    0.198 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Molecular Determinants of Selective and High-affinity Binding of the Scaffold Protein PDZK1 to the Urate Transporter URAT1.

Mymrikov, E.V.Wirth, C.Heinicke, J.I.Goll, J.Kern, B.A.Steck, C.Iaroslavtceva, A.K.Muhlethaler, T.Kottgen, A.Hunte, C.

(2025) J Mol Biology 438: 169615-169615

  • DOI: https://doi.org/10.1016/j.jmb.2025.169615
  • Primary Citation Related Structures: 
    9RXN, 9RXO, 9RXP, 9RXQ, 9RXR, 9RXS, 9RXT

  • PubMed Abstract: 

    The renal solute carrier URAT1 (SLC22A12) is essential for urate homeostasis, with loss-of-function linked to renal hypouricemia, nephrolithiasis and lower gout risk. URAT1 function depends on binding the multi-PDZ domain scaffold protein PDZK1 (NHERF3), with a similar role suggested for the related NHERF1. The molecular basis of these interactions remains poorly understood. Using fluorescence anisotropy, we show that full-length human PDZK1 binds the C-terminal peptide of URAT1 with high affinity (K D 170 nM), unlike NHERF1 (K D  > 70 µM). The PDZ1 domain of PDZK1 alone is sufficient for high-affinity binding (K D 160 nM), while PDZ4 provides a secondary site (K D 1.35 µM), with both interactions characterized by rapid kinetics. Gel filtration shows that PDZK1 can bind two URAT1 peptides. X-ray structures of individual PDZ domains from PDZK1 and NHERF1 complexed with the URAT1 peptide reveal the underlying molecular basis for selectivity and broad affinity range. Murine Pdzk1 and Nherf1 bind Urat1 with high affinity indicating species-specific interactions. These data provide insights into URAT1 regulation by PDZ scaffold proteins with relevance for understanding urate homeostasis regulation and related disorders.


  • Organizational Affiliation
    • Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany. Electronic address: evgeny.mymrikov@biochemie.uni-freiburg.de.

Macromolecule Content 

  • Total Structure Weight: 9.95 kDa 
  • Atom Count: 907 
  • Modeled Residue Count: 90 
  • Deposited Residue Count: 90 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Na(+)/H(+) exchange regulatory cofactor NHE-RF1,Sodium-dependent phosphate transport protein 2A90Homo sapiensMutation(s): 0 
Gene Names: NHERF1NHERFSLC9A3R1SLC34A1NPT2SLC17A2
UniProt & NIH Common Fund Data Resources
Find proteins for O14745 (Homo sapiens)
Explore O14745 
Go to UniProtKB:  O14745
PHAROS:  O14745
GTEx:  ENSG00000109062 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14745
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TOE

Query on TOE



Download:Ideal Coordinates CCD File
B [auth A]2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL
C7 H16 O4
JLGLQAWTXXGVEM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.36 Å
  • R-Value Free:  0.198 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.156 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.187α = 90
b = 64.187β = 90
c = 64.187γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata processing
Cootmodel building
PHASERphasing
MxCuBEdata collection
MolProbitymodel building
autoPROCdata reduction
autoPROCdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB 1453 (Project ID 431984000)
Germanys Excellence StrategyGermanyEXC-2189 (Project ID 390939984)
German Research Foundation (DFG)GermanySFB 1381 (Project ID 403222702)

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Database references