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- PDB-1i92: STRUCTURAL BASIS OF THE NHERF PDZ1-CFTR INTERACTION -

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Basic information

Entry
Database: PDB / ID: 1i92
TitleSTRUCTURAL BASIS OF THE NHERF PDZ1-CFTR INTERACTION
ComponentsNA+/H+ EXCHANGE REGULATORY CO-FACTOR
KeywordsSIGNALING PROTEIN / PDZ / CFTR / NHERF / COMPLEX
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 / bile acid secretion ...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 / bile acid secretion / maintenance of epithelial cell apical/basal polarity / import across plasma membrane / regulation of protein kinase activity / gamma-aminobutyric acid import / stereocilium tip / plasma membrane organization / phospholipase C-activating dopamine receptor signaling pathway / cilium organization / channel activator activity / gland morphogenesis / establishment of Golgi localization / fibroblast migration / intracellular phosphate ion homeostasis / plasma membrane protein complex / establishment of epithelial cell apical/basal polarity / type 3 metabotropic glutamate receptor binding / negative regulation of fibroblast migration / auditory receptor cell stereocilium organization / chloride channel regulator activity / negative regulation of mitotic cell cycle / beta-2 adrenergic receptor binding / negative regulation of platelet-derived growth factor receptor signaling pathway / growth factor receptor binding / nuclear migration / regulation of cell size / renal absorption / microvillus membrane / microvillus / phosphatase binding / transport across blood-brain barrier / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / ruffle / sperm midpiece / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endomembrane system / morphogenesis of an epithelium / cell periphery / protein localization to plasma membrane / filopodium / PDZ domain binding / 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 / regulation of cell shape / actin cytoskeleton / 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)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKarthikeyan, S. / Leung, T. / Ladias, J.A.A.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Structural basis of the Na+/H+ exchanger regulatory factor PDZ1 interaction with the carboxyl-terminal region of the cystic fibrosis transmembrane conductance regulator.
Authors: Karthikeyan, S. / Leung, T. / Ladias, J.A.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of the PDZ1 Domain of Human Na+/H+ Exchanger Regulatory Factor Provides Insights into the Mechanism of Carboxyl-terminal Leucine Recognition by Class I PDZ Domains
Authors: Karthikeyan, S. / Leung, T. / Birrane, G. / Webster, G. / Ladias, J.A.A.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: NHE-RF, A Regulatory Cofactor for NA(+)-H+ Exchange, is a Common Interactor for Merlin and ERM (MERM) Proteins
Authors: Murthy, A. / Gonzalez-Agosti, C. / Cordero, E. / Pinney, D. / Candia, C. / Solomon, F. / Gusella, J. / Ramesh, V.
#3: Journal: FEBS Lett. / Year: 1998
Title: Peptide Binding Consensus of the NHE-RF-PDZ1 Domain Matches the C-terminal Sequence of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)
Authors: Wang, S. / W Raab, R. / Schatz, P.J. / Guggino, W.B. / Li, M.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: A C-terminal Motif Found in the Beta2-Adrenergic Receptor, P2Y1 Receptor and Cystic Fibrosis Transmembrane Conductance Regulator Determines Binding to the Na+/H+ Exchanger Regulatory Factor Family of PDZ Proteins
Authors: Hall, R.A. / Ostedgaard, L.S. / Premont, R.T. / Blitzer, J.T. / Rahman, N. / Welsh, M.J. / Lefkowitz, R.J.
History
DepositionMar 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NA+/H+ EXCHANGE REGULATORY CO-FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0423
Polymers9,9711
Non-polymers712
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.658, 51.658, 66.966
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein NA+/H+ EXCHANGE REGULATORY CO-FACTOR / NHE-RF


Mass: 9971.442 Da / Num. of mol.: 1 / Fragment: PDZ1 DOMAIN (RESIDUES 11-94)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHERF / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O14745, GenBank: 4502785
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Sodium Acetate, Sodium Chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
20.1 Msodium acetate1reservoir
32 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 20, 2000 / Details: Mirrors
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→26.81 Å / Num. all: 11173 / Num. obs: 10950 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 27.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4 / Num. unique all: 885 / % possible all: 39.7
Reflection
*PLUS
Num. measured all: 110148
Reflection shell
*PLUS
% possible obs: 40 % / Rmerge(I) obs: 0.3

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G9O

1g9o


Resolution: 1.7→26.81 Å / SU B: 2.994 / SU ML: 0.099 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.109 / Stereochemistry target values: Engh & Huber
Details: Maximum Likelihood Refinement, Hydrogens have been added in the riding position, Residues from 81 to 85 refined with 2 conformations
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1065 9.7 %RANDOM
Rwork0.187 ---
all0.21 11173 --
obs0.1909 9885 92.63 %-
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms700 0 2 57 759
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.021
X-RAY DIFFRACTIONp_plane_restr0.0080.02
X-RAY DIFFRACTIONp_chiral_restr0.10.2
X-RAY DIFFRACTIONp_mcbond_it1.471.47
X-RAY DIFFRACTIONp_mcangle_it2.6342.634
X-RAY DIFFRACTIONp_scbond_it3.3993.399
X-RAY DIFFRACTIONp_scangle_it5.3215.321
LS refinement shellResolution: 1.7→1.74 Å /
RfactorNum. reflection
Rfree0.396 35
Rwork0.28 -
obs-399
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.7 % / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.8

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