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- PDB-2m0u: Complex structure of C-terminal CFTR peptide and extended PDZ1 do... -

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Basic information

Entry
Database: PDB / ID: 2m0u
TitleComplex structure of C-terminal CFTR peptide and extended PDZ1 domain from NHERF1
Components
  • C-terminal CFTR peptide
  • Na(+)/H(+) exchange regulatory cofactor NHE-RF1
KeywordsPEPTIDE BINDING PROTEIN/PROTEIN BINDING / PDZ domain / PEPTIDE BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


dopamine receptor binding / import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import ...dopamine receptor binding / import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / positive regulation of monoatomic ion transmembrane transport / bile acid secretion / maintenance of epithelial cell apical/basal polarity / intracellular phosphate ion homeostasis / cilium organization / plasma membrane organization / stereocilium tip / 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 / chloride channel regulator activity / negative regulation of platelet-derived growth factor receptor signaling pathway / auditory receptor cell stereocilium organization / nuclear migration / regulation of protein kinase activity / beta-2 adrenergic receptor binding / 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 / endomembrane system / phosphatase binding / protein-membrane adaptor activity / positive regulation of intrinsic apoptotic signaling pathway / sperm midpiece / ruffle / filopodium / PDZ domain binding / cell periphery / protein localization to plasma membrane / 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 / simulated annealing
AuthorsBhattacharya, S. / Ju, J.H. / Cowburn, D. / Bu, Z.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Ligand-Induced Dynamic Changes in Extended PDZ Domains from NHERF1.
Authors: Bhattacharya, S. / Ju, J.H. / Orlova, N. / Khajeh, J.A. / Cowburn, D. / Bu, Z.
History
DepositionNov 6, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Jul 17, 2013Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF1
B: C-terminal CFTR peptide


Theoretical massNumber of molelcules
Total (without water)13,4552
Polymers13,4552
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1fewest violations

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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: 12822.609 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): Rosetta 2 (DE3) / References: UniProt: O14745
#2: Protein/peptide C-terminal CFTR peptide


Mass: 632.687 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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 aliphatic
1312D 1H-13C HSQC aromatic
1413D 1H-15N NOESY
1513D 1H-13C NOESY aliphatic
1613D 1H-13C NOESY aromatic
1713D HNCA
1813D CBCA(CO)NH
1913D HBHA(CO)NH
11013D HN(CA)CB
11113D HNCO
11213D (H)CCH-TOCSY
11314D 13C,15N NOESY
11414D 13C,13C NOESY aliphatic
11512D 13C,15N f1,f2-filtered NOESY
11612D 13C,15N f2-filtered NOESY

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Sample preparation

DetailsContents: 286 uM [U-99% 13C; U-99% 15N] PDZ1, 20 mM TRIS, 150 mM sodium chloride, 0.5 mM DTT, 0.5 mM EDTA, 275 uM CFTR, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
286 uMPDZ1-1[U-99% 13C; U-99% 15N]1
20 mMTRIS-21
150 mMsodium chloride-31
0.5 mMDTT-41
0.5 mMEDTA-51
275 uMCFTR-61
Sample conditionsIonic strength: 150 / pH: 7.5 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.5Keller and Wuthrichdata analysis
CARA1.5Keller and Wuthrichpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
TALOS1.01Cornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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