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

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Basic information

Entry
Database: PDB / ID: 9rxq
TitleStructure of the PDZ1 domain from human NHERF1 with the C-terminal residues (KSTQF) of human URAT1 transporter (SLC22A12)
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF1,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


renal phosphate ion absorption / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / Defective SLC22A12 causes renal hypouricemia 1 (RHUC1) / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly ...renal phosphate ion absorption / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / Defective SLC22A12 causes renal hypouricemia 1 (RHUC1) / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / Organic anion transport by SLC22 transporters / maintenance of epithelial cell apical/basal polarity / regulation of protein kinase activity / bile acid secretion / import across plasma membrane / stereocilium tip / gamma-aminobutyric acid import / plasma membrane organization / phospholipase C-activating dopamine receptor signaling pathway / channel activator activity / renal urate salt excretion / gland morphogenesis / cilium organization / urate transport / urate metabolic process / urate transmembrane transporter activity / establishment of Golgi localization / intracellular phosphate ion homeostasis / fibroblast migration / establishment of epithelial cell apical/basal polarity / plasma membrane protein complex / organic anion transport / type 3 metabotropic glutamate receptor binding / cellular homeostasis / negative regulation of fibroblast migration / auditory receptor cell stereocilium organization / negative regulation of mitotic cell cycle / chloride channel regulator activity / beta-2 adrenergic receptor binding / growth factor receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / nuclear migration / microvillus membrane / renal absorption / regulation of cell size / microvillus / phosphatase binding / transport across blood-brain barrier / positive regulation of intrinsic apoptotic signaling pathway / ruffle / protein-membrane adaptor activity / monoatomic ion transport / sperm midpiece / endomembrane system / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / morphogenesis of an epithelium / cell periphery / protein localization to plasma membrane / PDZ domain binding / filopodium / brush border membrane / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / negative regulation of ERK1 and ERK2 cascade / cellular response to insulin stimulus / Wnt signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / regulation of cell shape / actin cytoskeleton / actin cytoskeleton organization / protein-containing complex assembly / vesicle / apical plasma membrane / response to xenobiotic stimulus / signaling receptor binding / negative regulation of cell population proliferation / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / PDZ domain ...EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / 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
ACETATE ION / Na(+)/H(+) exchange regulatory cofactor NHE-RF1 / Solute carrier family 22 member 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsWirth, C. / Mymrikov, E.V. / Hunte, C. / Heinicke, J.I.
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-RF1,Solute carrier family 22 member 12
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF1,Solute carrier family 22 member 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6963
Polymers19,6362
Non-polymers591
Water4,396244
1
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF1,Solute carrier family 22 member 12


Theoretical massNumber of molelcules
Total (without water)9,8181
Polymers9,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF1,Solute carrier family 22 member 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8772
Polymers9,8181
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.923, 51.469, 63.266
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-RF1,Solute carrier family 22 member 12 / 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 / Organic anion transporter 4-like protein / Renal-specific transporter / RST / Urate anion exchanger 1 / URAT1 / Urate:anion antiporter SLC22A12


Mass: 9818.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PDZ1 domain of human NHERF1 fused to, at its C-terminus, the five last residues (KSTQF) of the human URAT1 transporter (SLC22A12). The N-terminal glycine is left over after TEV cleavage. ...Details: PDZ1 domain of human NHERF1 fused to, at its C-terminus, the five last residues (KSTQF) of the human URAT1 transporter (SLC22A12). The N-terminal glycine is left over after TEV cleavage.,PDZ1 domain of human NHERF1 fused to, at its C-terminus, the five last residues (KSTQF) of the human URAT1 transporter (SLC22A12). The N-terminal glycine is left over after TEV cleavage.
Source: (gene. exp.) Homo sapiens (human)
Gene: NHERF1, NHERF, SLC9A3R1, SLC22A12, OATL4, URAT1, UNQ6453/PRO34004
Plasmid: pET30a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O14745, UniProt: Q96S37
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 100 mM sodium acetate pH 4.8 200 mM ammonium acetate 24% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.38→40 Å / Num. obs: 32381 / % possible obs: 99.3 % / Redundancy: 86.8 % / Biso Wilson estimate: 13.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.01 / Net I/σ(I): 50.1
Reflection shellResolution: 1.38→1.41 Å / Redundancy: 56.3 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 9.1 / Num. unique obs: 1484 / CC1/2: 0.983 / Rpim(I) all: 0.085 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
MxCuBEdata collection
autoPROCdata processing
MolProbitymodel building
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→38.2 Å / SU ML: 0.1417 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 19.1694
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1826 1659 5.12 %
Rwork0.1604 30713 -
obs0.1616 32372 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.73 Å2
Refinement stepCycle: LAST / Resolution: 1.38→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 4 244 1628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01041471
X-RAY DIFFRACTIONf_angle_d1.04041993
X-RAY DIFFRACTIONf_chiral_restr0.0829218
X-RAY DIFFRACTIONf_plane_restr0.0099271
X-RAY DIFFRACTIONf_dihedral_angle_d13.561578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.420.30371270.2332401X-RAY DIFFRACTION95.11
1.42-1.470.24091320.18982563X-RAY DIFFRACTION100
1.47-1.520.20891420.17952514X-RAY DIFFRACTION100
1.52-1.580.18911480.17012529X-RAY DIFFRACTION99.96
1.58-1.660.24111310.17182577X-RAY DIFFRACTION100
1.66-1.740.23161430.16982526X-RAY DIFFRACTION100
1.74-1.850.20341410.16472592X-RAY DIFFRACTION100
1.85-20.15841200.1632574X-RAY DIFFRACTION100
2-2.20.19871370.14472584X-RAY DIFFRACTION100
2.2-2.510.17661350.15232592X-RAY DIFFRACTION100
2.51-3.170.17321400.15412631X-RAY DIFFRACTION99.93
3.17-38.20.15151630.15542630X-RAY DIFFRACTION96.48
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.31673835772-2.783507014310.01714803682557.522977293591.512630762493.184980633470.06456229217890.0449808854158-0.1270987878190.013136396067-0.1432575672080.496425764915-0.274706167501-0.2181204902580.05811826552430.0913638439914-0.005540537640220.005560526578690.08943048129440.001037805344910.137386188667-29.49355878297.82200755978-18.9799333703
25.33296948042-2.979370674342.96142133764.18957190453-1.66956792122.98110601438-0.1404139211460.00177401768527-0.4891361484130.0133241669470.03266560588720.2988509490590.0577763007010.07422852684840.05327735308410.110361469771-0.01615240284670.03159839973770.0979830201958-0.0003240983888550.145023749338-10.1276761437-5.58610090711-18.1478395377
31.54660934544-1.479179776620.2903129584968.37716975634-6.141451839626.90443132587-0.092174055284-0.02640356224940.2524535618610.390981783067-0.161405467738-0.524240748562-0.3167517101910.2675578667850.3284142603540.142710832146-0.0303033739501-0.05023630667250.121000512273-0.01601891559180.1903220324635.182947360437.68708757526-17.2632846839
44.02939427599-0.354147663835-0.2262061464634.1178955175-0.2629179129441.98561228983-0.0228538416394-0.646279919901-0.4642495946430.5744357320430.08643533661410.06922607249310.0473760217573-0.0350711557175-0.09897370205230.1652435996650.009463438773350.006046452558840.1235190396190.03099677579680.138189788946-0.884124862648-2.63707608285-11.7443547979
50.63745203598-1.668481594030.3653247503164.59363819296-1.486713200131.43284302899-0.06364014056951.21270945791-0.702689950644-1.331284135530.3146759710670.3063878657870.316314227809-0.129270919499-0.03158950600560.364855807828-0.0864863827289-0.02813438915480.398438079013-0.1386028397470.28107670041-11.3107900844-1.83379392777-27.7658411132
67.280810802670.7233561951925.370789815187.068204291370.928465585574.172780457630.0667035839419-0.339481581834-0.4910767592560.5953375429240.2252703018410.2819773470040.00393940782523-0.495287676838-0.2476618450170.1046278095980.02560583532710.0412693962090.1127233098810.002718328652450.139876797058-8.469881910262.6546079678-15.7561271268
73.59589218969-2.072202239162.601417489631.20589332178-1.711394234656.01296598045-0.369259689076-0.4802433348270.475766259190.5078495299320.0741349524051-0.156847198203-0.3292468372270.06353693189920.1467685593390.205224512270.00795041396391-0.02404966786930.173666723226-0.03003367557650.114871520893-1.637493793755.90954053453-10.2099156244
84.68456944617-6.40384225635-3.864761893139.358599359635.458764162964.749917181040.02623091252990.491020402186-0.2083416724950.148438427511-0.196481529750.0237129102412-0.129972190271-0.1513623709990.1144692390220.0839899320408-0.006311575433560.007711206284670.105911189480.019684187260.111907801515-0.2054544486414.04656975692-24.995748156
96.997853385952.495629108246.034013170613.603108333692.080376020475.583237304170.07857038536320.2615920274620.0663521193297-0.102304407965-0.0121213383355-0.09820259774420.1074520891550.220310576489-0.03654327267640.08607762052630.005306262551070.02986628024260.1091402072440.01751305858480.08832297681451.20442129802-0.307489576585-29.3596831967
107.89474390952-0.6637770872881.192409971287.05076017167-1.076573997297.240446896140.0364441932555-0.097805692815-0.3181710085760.2340307453550.0601312441088-0.2477414437860.5175200617820.142445397336-0.07897356998070.1215602336190.0112960684867-0.002894404142490.07742294611260.008040486231520.0923812821661-0.13684901807-7.50724790678-23.4044249496
115.32302417283-4.712441187242.96643896287.12742704862-4.314743695563.396283856890.06548561220730.0504189745387-0.1201031078150.0528364904649-0.0910931897251-0.1316139303480.09495418933320.1597552545330.06151512181060.087462078903-0.00655485671518-0.02060771986270.0960785025089-0.003716633056750.1167158489546.465042369520.675988132671-19.0473721814
125.28600095768-1.92020609409-6.226397503564.305579833511.471157266668.68446141629-0.06181521188480.1237674881230.2647103005230.02803096254670.045626444304-0.150658586356-0.164840713908-0.1143149153160.01982389309770.0835524608647-0.00829976268853-0.02033178838410.07051121968020.0107954376950.0992860556256-13.789717772415.2665402508-18.3995396961
136.34428635836-3.24296358407-0.9097870698318.13261541715.469831119817.361150218940.0472138266308-0.13454828178-0.1560054351130.291337389256-0.1656031412440.2987850251660.197318641272-0.324750267670.1943936085020.112948552823-0.03834124655310.01883833591580.1127618837440.01638134415960.194825068741-28.46564738231.35616396155-17.7216727548
144.286082520470.04942161806250.3833538017774.74668832260.008325657511673.468053250660.009962493590420.1363890807120.138885637976-0.0125196774824-0.00971573479663-0.0276393698819-0.1459625618660.0833086125325-0.04837980658880.0892144722697-0.00659604428215-0.006029826217890.04213006984070.01741665045360.0889761556564-19.29561890211.9894914348-17.8944011921
151.64505355993-0.1522230593050.1784844834492.60820921604-0.1133416082625.941766829510.047372290008-0.0822262532631-0.1014687166140.118252457258-0.04374029052080.01903744862660.0289864746918-0.06183157131340.000409665017820.0669573428819-0.00972467320002-0.0005173527399980.04834185143150.0008690791581750.088525809613-20.9126929535.13002906581-14.7161994293
165.087152248575.01115066796-1.014826448695.62160826247-2.581851642813.90178256629-0.0131672758280.5273646767240.0477963612039-0.3258423805640.1028764504790.1166439466760.200430077672-0.177807450496-0.07227551623140.1101590651990.0507897943266-0.05213302423830.160223572987-0.04270483059750.113600273157-25.3292751799.75100132402-29.0564779213
177.67620596491-1.429469054450.7603871868646.266030705690.6556910904847.36986545471-0.004476082860690.1322602226680.2337614966950.2124035628130.03166099090370.308268983136-0.420261104059-0.233973935650.0009417083381480.09223983595370.02524802411140.009127614448550.08706865518710.01770187931870.0996188368571-23.782259298317.1403446364-23.142882074
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 82 through 91 )BB82 - 9173 - 82
22chain 'B' and (resid 92 through 99 )BB92 - 9983 - 90
33chain 'A' and (resid 10 through 18 )AA10 - 181 - 9
44chain 'A' and (resid 19 through 29 )AA19 - 2910 - 20
55chain 'A' and (resid 30 through 37 )AA30 - 3721 - 28
66chain 'A' and (resid 38 through 42 )AA38 - 4229 - 33
77chain 'A' and (resid 43 through 57 )AA43 - 5734 - 48
88chain 'A' and (resid 58 through 62 )AA58 - 6249 - 53
99chain 'A' and (resid 63 through 71 )AA63 - 7154 - 62
1010chain 'A' and (resid 72 through 80 )AA72 - 8063 - 71
1111chain 'A' and (resid 81 through 91 )AA81 - 9172 - 82
1212chain 'A' and (resid 92 through 99 )AA92 - 9983 - 90
1313chain 'B' and (resid 10 through 18 )BB10 - 181 - 9
1414chain 'B' and (resid 19 through 37 )BB19 - 3710 - 28
1515chain 'B' and (resid 38 through 62 )BB38 - 6229 - 53
1616chain 'B' and (resid 63 through 71 )BB63 - 7154 - 62
1717chain 'B' and (resid 72 through 81 )BB72 - 8163 - 72

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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