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- PDB-2jxo: Structure of the second PDZ domain of NHERF-1 -

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Basic information

Entry
Database: PDB / ID: 2jxo
TitleStructure of the second PDZ domain of NHERF-1
ComponentsEzrin-radixin-moesin-binding phosphoprotein 50
KeywordsPROTEIN BINDING / NHERF-1 / PDZ domain / PDZ2 / Acetylation / Cell projection / Membrane / Phosphoprotein / Polymorphism / Wnt signaling pathway
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 / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / maintenance of epithelial cell apical/basal polarity ...renal phosphate ion absorption / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / maintenance of epithelial cell apical/basal polarity / import across plasma membrane / bile acid secretion / regulation of protein kinase activity / gamma-aminobutyric acid import / stereocilium tip / plasma membrane organization / phospholipase C-activating dopamine receptor signaling pathway / cilium organization / gland morphogenesis / channel activator activity / intracellular phosphate ion homeostasis / establishment of Golgi localization / fibroblast migration / plasma membrane protein complex / establishment of epithelial cell apical/basal polarity / negative regulation of fibroblast migration / type 3 metabotropic glutamate receptor binding / chloride channel regulator activity / auditory receptor cell stereocilium organization / negative regulation of mitotic cell cycle / negative regulation of platelet-derived growth factor receptor signaling pathway / beta-2 adrenergic receptor binding / growth factor receptor binding / nuclear migration / regulation of cell size / microvillus membrane / renal absorption / microvillus / phosphatase binding / transport across blood-brain barrier / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / sperm midpiece / ruffle / 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 / Wnt signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / actin cytoskeleton / regulation of cell shape / actin cytoskeleton organization / protein-containing complex assembly / vesicle / apical plasma membrane / signaling receptor binding / negative regulation of cell population proliferation / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / membrane / cytoplasm
Similarity search - Function
EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Na(+)/H(+) exchange regulatory cofactor NHE-RF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsCheng, H. / Li, J. / Dai, Z. / Bu, Z. / Roder, H.
CitationJournal: Structure / Year: 2009
Title: Autoinhibitory Interactions between the PDZ2 and C-terminal Domains in the Scaffolding Protein NHERF1
Authors: Cheng, H. / Li, J. / Fazlieva, R. / Dai, Z. / Bu, Z. / Roder, H.
History
DepositionNov 27, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ezrin-radixin-moesin-binding phosphoprotein 50


Theoretical massNumber of molelcules
Total (without water)10,7251
Polymers10,7251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 1000structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Ezrin-radixin-moesin-binding phosphoprotein 50 / EBP50 / Na+ / /H+ / exchange regulatory cofactor NHE-RF / NHERF-1 / Regulatory cofactor of Na+ / ...EBP50 / Na+ / /H+ / exchange regulatory cofactor NHE-RF / NHERF-1 / Regulatory cofactor of Na+ / /H+ / exchanger / Sodium-hydrogen exchanger regulatory factor 1 / Solute carrier family 9 isoform 3 regulatory factor 1


Mass: 10725.136 Da / Num. of mol.: 1 / Fragment: PDZ 2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A3R1, NHERF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14745

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-15N HSQC
1423D 1H-15N NOESY
1523D 1H-15N TOCSY
1623D HNHA
1733D HNCO
1833D HN(CA)CB
1933D HN(COCA)CB
11033D (H)CCH-COSY
11133D (H)CCH-TOCSY
11233D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM PDZ2, HEPES, DTT, H2O, DSS, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-100% 15N] PDZ2, HEPES, DTT, H2O, DSS, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-100% 13C; U-100% 15N] PDZ2, HEPES, DTT, H2O, DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPDZ2, HEPES, DTT, H2O, DSS1
1 mMPDZ2, HEPES, DTT, H2O, DSS[U-100% 15N]2
1 mMPDZ2, HEPES, DTT, H2O, DSS[U-100% 13C; U-100% 15N]3
Sample conditionsIonic strength: 0.15 / pH: 7.5 / Pressure: ambient / Temperature: 288.1 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000Accelrys Software Inc.processing
Felix2000Accelrys Software Inc.chemical shift calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinchemical shift calculation
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 12

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