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- PDB-9rxt: Structure of the PDZ1 domain from human NHERF1 with the C-termina... -

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Entry
Database: PDB / ID: 9rxt
TitleStructure of the PDZ1 domain from human NHERF1 with the C-terminal residues (NATRL) of the human sodium-dependent phosphate transporter 2A (NaPi-IIa, SLC34A1)
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF1,Sodium-dependent phosphate transport protein 2A
KeywordsPROTEIN BINDING / Scaffold protein / PDZ domain / phosphate transport / solute carrier / protein-protein interaction / NHERFs
Function / homology
Function and homology information


gentamycin metabolic process / positive regulation of phosphate transmembrane transport / Type II Na+/Pi cotransporters / Defective SLC34A1 causes hypophosphatemic nephrolithiasis/osteoporosis 1 (NPHLOP1) / arsenate ion transmembrane transport / sodium:phosphate symporter activity / sodium-dependent phosphate transport / indole metabolic process / positive regulation of sodium-dependent phosphate transport / renal phosphate ion absorption ...gentamycin metabolic process / positive regulation of phosphate transmembrane transport / Type II Na+/Pi cotransporters / Defective SLC34A1 causes hypophosphatemic nephrolithiasis/osteoporosis 1 (NPHLOP1) / arsenate ion transmembrane transport / sodium:phosphate symporter activity / sodium-dependent phosphate transport / indole metabolic process / positive regulation of sodium-dependent phosphate transport / renal phosphate ion absorption / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / dentinogenesis / cellular response to metal ion / cerebrospinal fluid circulation / negative regulation of sodium ion transport / glycoprotein metabolic process / microvillus assembly / maintenance of epithelial cell apical/basal polarity / regulation of protein kinase activity / response to peptide / bile acid secretion / import across plasma membrane / stereocilium tip / positive regulation of membrane potential / gamma-aminobutyric acid import / tricarboxylic acid metabolic process / plasma membrane organization / phospholipase C-activating dopamine receptor signaling pathway / response to thyroid hormone / channel activator activity / gland morphogenesis / cilium organization / response to mercury ion / response to potassium ion / phosphate ion homeostasis / phosphate ion transport / establishment of Golgi localization / intracellular phosphate ion homeostasis / fibroblast migration / cellular response to staurosporine / Surfactant metabolism / establishment of epithelial cell apical/basal polarity / plasma membrane protein complex / type 3 metabotropic glutamate receptor binding / negative regulation of fibroblast migration / cellular response to phosphate starvation / sodium ion import across plasma membrane / phosphate ion transmembrane transport / auditory receptor cell stereocilium organization / response to vitamin A / negative regulation of mitotic cell cycle / chloride channel regulator activity / response to growth hormone / beta-2 adrenergic receptor binding / growth factor receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / cellular response to parathyroid hormone stimulus / nuclear migration / microvillus membrane / renal absorption / regulation of cell size / microvillus / brush border / response to magnesium ion / response to cadmium ion / phosphatase binding / transport across blood-brain barrier / positive regulation of intrinsic apoptotic signaling pathway / ruffle / protein-membrane adaptor activity / sperm midpiece / endomembrane system / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ossification / morphogenesis of an epithelium / cell periphery / protein localization to plasma membrane / PDZ domain binding / filopodium / kidney development / brush border membrane / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / negative regulation of ERK1 and ERK2 cascade / response to lead ion / Wnt signaling pathway / mitotic spindle / response to estradiol / adenylate cyclase-activating dopamine receptor signaling pathway / regulation of cell shape / actin cytoskeleton / actin cytoskeleton organization / protein-containing complex assembly / vesicle / endosome
Similarity search - Function
Sodium-dependent phosphate transport protein / Na+/Pi-cotransporter / EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Na(+)/H(+) exchange regulatory cofactor NHE-RF1 / Sodium-dependent phosphate transport protein 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsWirth, C. / Kern, B.A. / Mymrikov, E.V. / Hunte, C.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB 1453 (Project ID 431984000) Germany
Germanys Excellence StrategyEXC-2189 (Project ID 390939984) Germany
German Research Foundation (DFG)SFB 1381 (Project ID 403222702) Germany
Citation
Journal: J.Mol.Biol. / Year: 2025
Title: Molecular determinants of selective and high-affinity binding of the scaffold protein PDZK1 to the urate transporter URAT1.
Authors: Mymrikov, E.V. / Wirth, C. / Heinicke, J.I. / Goll, J. / Kern, B.A. / Steck, C. / Iaroslavtceva, A.K. / Muhlethaler, T. / Kottgen, A. / Hunte, C.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF1,Sodium-dependent phosphate transport protein 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9462
Polymers9,7821
Non-polymers1641
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, fluorescence anisotropy assay, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.187, 64.187, 64.187
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-284-

HOH

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Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF1,Sodium-dependent phosphate transport protein 2A / NHERF-1 / Ezrin-radixin-moesin-binding phosphoprotein 50 / EBP50 / Regulatory cofactor of Na(+)/H(+) ...NHERF-1 / Ezrin-radixin-moesin-binding phosphoprotein 50 / EBP50 / Regulatory cofactor of Na(+)/H(+) exchanger / Sodium-hydrogen exchanger regulatory factor 1 / Solute carrier family 9 isoform A3 regulatory factor 1 / Sodium-phosphate transport protein 2A / Na(+)-dependent phosphate cotransporter 2A / NaPi-3 / Sodium/phosphate cotransporter 2A / Na(+)/Pi cotransporter 2A / NaPi-2a / Solute carrier family 34 member 1


Mass: 9782.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PDZ1 domain of human NHERF1 fused, at its C-terminus, to the five last residues (NATRL) of the human sodium-dependent phosphate transporter 2A (NaPi-IIa, SLC34A1). The N-terminal glycine is ...Details: PDZ1 domain of human NHERF1 fused, at its C-terminus, to the five last residues (NATRL) of the human sodium-dependent phosphate transporter 2A (NaPi-IIa, SLC34A1). The N-terminal glycine is left over after TEV cleavage.,PDZ1 domain of human NHERF1 fused, at its C-terminus, to the five last residues (NATRL) of the human sodium-dependent phosphate transporter 2A (NaPi-IIa, SLC34A1). The N-terminal glycine is left over after TEV cleavage.
Source: (gene. exp.) Homo sapiens (human) / Gene: NHERF1, NHERF, SLC9A3R1, SLC34A1, NPT2, SLC17A2 / Plasmid: pET30a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14745, UniProt: Q06495
#2: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 100mM Bicine pH 9, 100mM NaCl, 30% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 27, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 1.36→38 Å / Num. obs: 19221 / % possible obs: 99.8 % / Redundancy: 120 % / Biso Wilson estimate: 18.79 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.11 / Net I/σ(I): 30.3
Reflection shellResolution: 1.36→1.383 Å / Redundancy: 75.7 % / Rmerge(I) obs: 3.78 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 904 / CC1/2: 0.584 / Rpim(I) all: 0.417 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROC1.0.5data processing
Coot0.9.6model building
PHASER2.8.3phasing
MxCuBEdata collection
MolProbitymodel building
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→37.06 Å / SU ML: 0.1492 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8919
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1975 872 4.55 %
Rwork0.1553 18300 -
obs0.1572 19172 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.45 Å2
Refinement stepCycle: LAST / Resolution: 1.36→37.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms687 0 11 147 845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074777
X-RAY DIFFRACTIONf_angle_d0.9431057
X-RAY DIFFRACTIONf_chiral_restr0.0709115
X-RAY DIFFRACTIONf_plane_restr0.0083146
X-RAY DIFFRACTIONf_dihedral_angle_d15.9673317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.440.26391330.18242950X-RAY DIFFRACTION97.63
1.45-1.560.22221290.12883054X-RAY DIFFRACTION100
1.56-1.710.2261550.19013020X-RAY DIFFRACTION99.97
1.71-1.960.20081530.17453032X-RAY DIFFRACTION99.97
1.96-2.470.17431330.16993097X-RAY DIFFRACTION99.97
2.47-37.060.19571690.14043147X-RAY DIFFRACTION100

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