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- PDB-9rxo: Structure of the PDZ2 domain from human PDZK1 (NHERF3) with the C... -

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Basic information

Entry
Database: PDB / ID: 9rxo
TitleStructure of the PDZ2 domain from human PDZK1 (NHERF3) with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12)
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF3,Solute carrier family 22 member 12
KeywordsPROTEIN BINDING / Scaffold protein / PDZ domain / urate transporter / solute carrier / protein-protein interaction / NHERFs
Function / homology
Function and homology information


carnitine transmembrane transport / Defective SLC22A12 causes renal hypouricemia 1 (RHUC1) / Organic anion transport by SLC22 transporters / scavenger receptor binding / renal urate salt excretion / urate transport / urate metabolic process / urate transmembrane transporter activity / organic anion transport / xenobiotic detoxification by transmembrane export across the plasma membrane ...carnitine transmembrane transport / Defective SLC22A12 causes renal hypouricemia 1 (RHUC1) / Organic anion transport by SLC22 transporters / scavenger receptor binding / renal urate salt excretion / urate transport / urate metabolic process / urate transmembrane transporter activity / organic anion transport / xenobiotic detoxification by transmembrane export across the plasma membrane / cellular homeostasis / positive regulation of protein localization to membrane / microvillus membrane / brush border / positive regulation of protein targeting to membrane / transporter activator activity / protein-membrane adaptor activity / monoatomic ion transport / regulation of monoatomic anion transport / protein localization to plasma membrane / PDZ domain binding / brush border membrane / cellular response to insulin stimulus / apical plasma membrane / response to xenobiotic stimulus / signaling receptor binding / protein-containing complex binding / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Na(+)/H(+) exchange regulatory cofactor NHE-RF3 / Solute carrier family 22 member 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsWirth, C. / 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF3,Solute carrier family 22 member 12
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF3,Solute carrier family 22 member 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0433
Polymers19,9812
Non-polymers621
Water4,936274
1
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF3,Solute carrier family 22 member 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0522
Polymers9,9901
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF3,Solute carrier family 22 member 12


Theoretical massNumber of molelcules
Total (without water)9,9901
Polymers9,9901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.618, 39.105, 137.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF3,Solute carrier family 22 member 12 / NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi ...NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi cotransporter C-terminal-associated protein 1 / NaPi-Cap1 / PDZ domain-containing protein 1 / Sodium-hydrogen exchanger regulatory factor 3 / Organic anion transporter 4-like protein / Renal-specific transporter / RST / Urate anion exchanger 1 / URAT1 / Urate:anion antiporter SLC22A12


Mass: 9990.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PDZ2 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (KSTQF). The N-terminal glycine is left over after TEV cleavage.,PDZ2 ...Details: PDZ2 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (KSTQF). The N-terminal glycine is left over after TEV cleavage.,PDZ2 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (KSTQF). The N-terminal glycine is left over after TEV cleavage.
Source: (gene. exp.) Homo sapiens (human)
Gene: PDZK1, CAP70, NHERF3, PDZD1, SLC22A12, OATL4, URAT1, UNQ6453/PRO34004
Plasmid: pET30a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5T2W1, UniProt: Q96S37
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 26% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: May 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.2→35 Å / Num. obs: 49076 / % possible obs: 94.1 % / Redundancy: 10.1 % / Biso Wilson estimate: 14.55 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.028 / Net I/σ(I): 12.1
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 1.415 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2304 / CC1/2: 0.562 / Rpim(I) all: 0.479

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROC1.0.5data processing
STARANISO2.4.9data scaling
PHASER2.8.3phasing
MxCuBEdata collection
Coot0.9.8.3model building
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→34.45 Å / SU ML: 0.1294 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.5352
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2035 2297 5 %
Rwork0.1656 43644 -
obs0.1675 45941 81.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.17 Å2
Refinement stepCycle: LAST / Resolution: 1.2→34.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 4 274 1676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861498
X-RAY DIFFRACTIONf_angle_d1.03742021
X-RAY DIFFRACTIONf_chiral_restr0.0803225
X-RAY DIFFRACTIONf_plane_restr0.0105266
X-RAY DIFFRACTIONf_dihedral_angle_d15.0431582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.220.4424730.3561195X-RAY DIFFRACTION36.25
1.22-1.250.3154840.26331624X-RAY DIFFRACTION48.94
1.25-1.280.2903890.21671761X-RAY DIFFRACTION53.5
1.28-1.320.2241910.19922014X-RAY DIFFRACTION60.11
1.32-1.360.21161280.16242309X-RAY DIFFRACTION69.53
1.36-1.40.24281480.1742479X-RAY DIFFRACTION75.64
1.4-1.450.21041370.16532889X-RAY DIFFRACTION86.31
1.45-1.510.20521600.16113051X-RAY DIFFRACTION91.25
1.51-1.580.19781560.16523179X-RAY DIFFRACTION95.34
1.58-1.660.18881710.15413340X-RAY DIFFRACTION99.97
1.66-1.760.19431660.14653312X-RAY DIFFRACTION98.14
1.76-1.90.18491850.14733238X-RAY DIFFRACTION96.64
1.9-2.090.1921710.14723097X-RAY DIFFRACTION92.24
2.09-2.390.19991810.15013336X-RAY DIFFRACTION98.02
2.39-3.020.20921700.17013385X-RAY DIFFRACTION97.5
3.02-34.450.19921870.17623435X-RAY DIFFRACTION95.27

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