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- PDB-2krg: Solution Structure of human sodium/ hydrogen exchange regulatory ... -

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Basic information

Entry
Database: PDB / ID: 2krg
TitleSolution Structure of human sodium/ hydrogen exchange regulatory factor 1(150-358)
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF1
KeywordsSIGNALING PROTEIN / Acetylation / Cell projection / Disease mutation / Membrane / Phosphoprotein / Polymorphism / Wnt signaling pathway
Function / homology
Function and homology information


import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import ...import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / cerebrospinal fluid circulation / microvillus assembly / positive regulation of monoatomic ion transmembrane transport / negative regulation of sodium ion transport / bile acid secretion / maintenance of epithelial cell apical/basal polarity / plasma membrane organization / stereocilium tip / intracellular phosphate ion homeostasis / cilium organization / gland morphogenesis / myosin II binding / phospholipase C-activating dopamine receptor signaling pathway / growth factor receptor binding / establishment of Golgi localization / fibroblast migration / type 3 metabotropic glutamate receptor binding / plasma membrane protein complex / establishment of epithelial cell apical/basal polarity / negative regulation of fibroblast migration / negative regulation of platelet-derived growth factor receptor signaling pathway / chloride channel regulator activity / auditory receptor cell stereocilium organization / nuclear migration / regulation of protein kinase activity / microvillus membrane / regulation of cell size / renal absorption / microvillus / transport across blood-brain barrier / negative regulation of mitotic cell cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatase binding / endomembrane system / beta-2 adrenergic receptor binding / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / sperm midpiece / ruffle / filopodium / protein localization to plasma membrane / cell periphery / PDZ domain binding / morphogenesis of an epithelium / brush border membrane / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / beta-catenin binding / Wnt signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / : / actin cytoskeleton / regulation of cell shape / actin cytoskeleton organization / protein-containing complex assembly / vesicle / transmembrane transporter binding / apical plasma membrane / negative regulation of cell population proliferation / signaling receptor binding / protein-containing complex binding / perinuclear region of cytoplasm / extracellular exosome / membrane / identical protein binding / 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 / PDZ superfamily ...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 / torsion angle dynamics, simulated annealing
AuthorsBhattacharya, S. / Dai, Z. / Li, J. / Baxter, S. / Callaway, D.J.E. / Cowburn, D. / Bu, Z.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: A conformational switch in the scaffolding protein NHERF1 controls autoinhibition and complex formation.
Authors: Bhattacharya, S. / Dai, Z. / Li, J. / Baxter, S. / Callaway, D.J.E. / Cowburn, D. / Bu, Z.
History
DepositionDec 17, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: 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_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF1


Theoretical massNumber of molelcules
Total (without water)23,6691
Polymers23,6691
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)20 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF1 / 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


Mass: 23669.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A3R1, NHERF, NHERF1 / Plasmid: pET151/D-TOPO / 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-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCA
1613D HN(CO)CA
1713D HNCO
1823D HN(CA)CB
1933D HN(CA)CB
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11233D 1H-15N NOESY
11333D 1H-13C NOESY
11413D H(CCO)NH
11513D (H)CCH-TOCSY
11613D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
1557 uM [U-100% 13C; U-100% 15N] NHERF1 (150-358), 20 mM HEPES, 150 mM sodium chloride, 0.5 mM DTT, 0.1 mM PMSF, 90% H2O/10% D2O90% H2O/10% D2O
2389 uM [U-100% 13C; U-100% 15N; U-80% 2H] NHERF1 (150-358), 20 mM HEPES, 150 mM sodium chloride, 0.5 mM DTT, 0.1 mM PMSF, 90% H2O/10% D2O90% H2O/10% D2O
3413 uM [U-100% 13C; U-100% 15N]-Leu,Val,Phe NHERF1 (150-358), 20 mM HEPES, 150 mM sodium chloride, 0.5 mM DTT, 0.1 mM PMSF, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
557 uMNHERF1 (150-358)[U-100% 13C; U-100% 15N]1
20 mMHEPES1
150 mMsodium chloride1
0.5 mMDTT1
0.1 mMPMSF1
389 uMNHERF1 (150-358)[U-100% 13C; U-100% 15N; U-80% 2H]2
20 mMHEPES2
150 mMsodium chloride2
0.5 mMDTT2
0.1 mMPMSF2
413 uMNHERF1 (150-358)[U-100% 13C; U-100% 15N]-Leu,Val,Phe3
20 mMHEPES3
150 mMsodium chloride3
0.5 mMDTT3
0.1 mMPMSF3
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1.3Bruker Biospincollection
TopSpin2.1.3Bruker Biospinprocessing
CARA1.5Keller, R. et al.data analysis
CARA1.5Keller, R. et al.chemical shift assignment
CYANA2.1Guntert, P. et al.structure solution
X-PLOR NIH2.24Schwieters, C. et al.structure solution
X-PLOR NIH2.24Schwieters, C. et al.refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: Automated NOE Assignment in CYANA, Final refinement in XPLOR-NIH
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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