[English] 日本語
Yorodumi
- PDB-9rxr: Structure of the PDZ1 domain from human PDZK1 (NHERF3) with the C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rxr
TitleStructure of the PDZ1 domain from human PDZK1 (NHERF3) with the C-terminal residues (VLKSTQF) 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: 1.69 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
CitationJournal: 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.
History
DepositionJul 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,2541
Polymers12,2541
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, interaction analysed using fluorescence anisotropy assays., gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.887, 35.887, 72.069
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

-
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: 12253.968 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PDZ1 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (VLKSTQF). The N-terminal glycine is left over after TEV cleavage. ...Details: PDZ1 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (VLKSTQF). The N-terminal glycine is left over after TEV cleavage.,PDZ1 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (VLKSTQF). The N-terminal glycine is left over after TEV cleavage.,PDZ1 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (VLKSTQF). The N-terminal glycine is left over after TEV cleavage.,PDZ1 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (VLKSTQF). The N-terminal glycine is left over after TEV cleavage.,PDZ1 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (VLKSTQF). The N-terminal glycine is left over after TEV cleavage.,PDZ1 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (VLKSTQF). The N-terminal glycine is left over after TEV cleavage.,PDZ1 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (VLKSTQF). The N-terminal glycine is left over after TEV cleavage.,PDZ1 domain of human PDZK1 (NHERF3) fused to, at its C-terminus, the seven last residues of the human URAT1 transporter (VLKSTQF). 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES, pH 6.5, 700 mM NaCl, 18% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 18, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→31.1 Å / Num. obs: 9092 / % possible obs: 93 % / Redundancy: 42.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.024 / Net I/σ(I): 16.7
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 37 % / Rmerge(I) obs: 1.958 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 455 / CC1/2: 0.906 / Rpim(I) all: 0.325 / % possible all: 86.8

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROC1.0.5data processing
MxCuBEdata collection
PHASER2.8.3phasing
Coot0.9.8.3model building
MolProbitymodel building
XDSdata reduction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→31.08 Å / SU ML: 0.1628 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.3223
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2105 398 4.38 %
Rwork0.187 8693 -
obs0.188 9091 78.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.2 Å2
Refinement stepCycle: LAST / Resolution: 1.69→31.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 0 83 942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021914
X-RAY DIFFRACTIONf_angle_d0.46551232
X-RAY DIFFRACTIONf_chiral_restr0.0385137
X-RAY DIFFRACTIONf_plane_restr0.005164
X-RAY DIFFRACTIONf_dihedral_angle_d13.6743368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.940.3025830.27591438X-RAY DIFFRACTION39.21
1.94-2.440.27591570.22483559X-RAY DIFFRACTION96
2.44-31.080.17431580.16273696X-RAY DIFFRACTION100
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)
14.91506204099-3.22986925827-2.730410085177.189210521456.615276439957.053797338430.1680766669150.393887391991-0.201167492483-0.340159746217-0.01816631082960.25857982930.279589585295-0.56457478942-0.1345436002970.286589537003-0.111110570433-0.0770298014170.2698303186630.049803461590.22342647746-12.8986654932-7.933307624335.25866273362
25.00995078853-0.678302202369-0.01935456854294.60495069166-0.09209589798193.46700904837-0.049811406026-0.52566284345-0.4301684940450.3340509598180.2175076768640.3480385517740.569481921138-0.454448673462-0.135149121940.266422576207-0.0541935261566-0.03168720056280.2524396237860.046359884650.153476960164-8.34140881368-5.6234735680617.5192909043
32.88950858230.195568684249-0.1251137005763.53822647817-2.037029680323.318704710720.364518467983-0.139017207933-0.180910793583-0.0104537752191-0.159471660548-0.06978433866880.7901336775460.0829996793221-0.02730352155150.25779394277-0.0418505382494-0.04709444861650.1194794210040.0246293537560.100240419126-2.50270107356-6.063514063297.50442901606
44.21210010336-3.050373171480.464298946062.78524326372-0.7789989224262.875866052440.121873945299-0.1509114757850.2910169787620.0190368326267-0.0702972049169-0.0778790547556-0.00985237148055-0.185637391292-0.01711223554090.160794466265-0.02998878563410.01808412900250.09046380569280.02846811725240.101597335787-5.321534958021.0403967897910.5971097256
51.93423118999-1.107601212510.6871194857863.13269103535-0.8690100026521.729140091070.116147552463-0.0583861568205-0.30521815203-0.0425346169039-0.007365091243590.01484805226820.3199901555390.0664402947743-0.05169070347360.9651474860120.280511803908-0.2339005992910.0276867697920.174932242920.106606194801-0.389381600056-19.33248885095.97298840109
63.379345793622.25230330957-0.9463205981947.78983315007-2.504818659143.10444356444-0.01713605531510.115967966668-0.2270521224030.07597341103680.2148049629170.03507042097810.421279139070.0935203588383-0.1803313322380.234796134910.0338798338746-0.03314073156860.171624373955-0.001103683801450.104885067536-1.0124834127-6.55014011161-3.25804882631
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 13 )5 - 131 - 9
22chain 'A' and (resid 14 through 47 )14 - 4710 - 43
33chain 'A' and (resid 48 through 67 )48 - 6744 - 63
44chain 'A' and (resid 68 through 88 )68 - 8864 - 84
55chain 'A' and (resid 89 through 97 )89 - 9785 - 93
66chain 'A' and (resid 98 through 113 )98 - 11394 - 109

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more