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- PDB-1gq5: Structural Determinants of the NHERF Interaction with beta2-AR an... -

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Basic information

Entry
Database: PDB / ID: 1gq5
TitleStructural Determinants of the NHERF Interaction with beta2-AR and PDGFR
ComponentsEZRIN-RADIXIN-MOESIN BINDING PHOSPHOPROTEIN-50
KeywordsSIGNALING PROTEIN / PDZ / BETA2-ADRENERGIC RECEPTOR / PDGFR / NHERF / COMPLEX
Function / homology
Function and homology information


platelet-derived growth factor receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / platelet activating factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in vasculogenesis / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / renal phosphate ion absorption / type 2 metabotropic glutamate receptor binding / dopamine receptor binding ...platelet-derived growth factor receptor activity / cell migration involved in coronary angiogenesis / metanephric glomerular mesangial cell proliferation involved in metanephros development / platelet activating factor receptor activity / platelet-derived growth factor beta-receptor activity / cell migration involved in vasculogenesis / positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway / renal phosphate ion absorption / type 2 metabotropic glutamate receptor binding / dopamine receptor binding / smooth muscle cell chemotaxis / glutathione transport / metanephric glomerular capillary formation / microvillus assembly / cerebrospinal fluid circulation / aorta morphogenesis / retina vasculature development in camera-type eye / smooth muscle adaptation / maintenance of epithelial cell apical/basal polarity / platelet-derived growth factor binding / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / gland morphogenesis / plasma membrane organization / stereocilium tip / bile acid secretion / regulation of protein kinase activity / import across plasma membrane / vascular endothelial growth factor binding / gamma-aminobutyric acid import / channel activator activity / cilium organization / cardiac myofibril assembly / establishment of Golgi localization / Signaling by PDGF / chloride channel regulator activity / negative regulation of mitotic cell cycle / morphogenesis of an epithelium / positive regulation of chemotaxis / plasma membrane protein complex / establishment of epithelial cell apical/basal polarity / phospholipase C activator activity / type 3 metabotropic glutamate receptor binding / negative regulation of cell motility / platelet-derived growth factor receptor signaling pathway / platelet-derived growth factor receptor binding / beta-2 adrenergic receptor binding / positive regulation of smooth muscle cell migration / nuclear migration / growth factor receptor binding / positive regulation of DNA biosynthetic process / regulation of cell size / platelet-derived growth factor receptor-beta signaling pathway / renal absorption / microvillus membrane / positive regulation of MAP kinase activity / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of calcium ion import / microvillus / phosphatase binding / transport across blood-brain barrier / positive regulation of calcium-mediated signaling / ruffle / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / positive regulation of mitotic nuclear division / peptidyl-tyrosine phosphorylation / endomembrane system / lysosomal lumen / positive regulation of smooth muscle cell proliferation / Downstream signal transduction / cell surface receptor protein tyrosine kinase signaling pathway / sperm midpiece / protein localization to plasma membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of actin cytoskeleton organization / cell periphery / GTPase activator activity / cell chemotaxis / brush border membrane / filopodium / PDZ domain binding / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / receptor protein-tyrosine kinase / beta-catenin binding / positive regulation of reactive oxygen species metabolic process / Constitutive Signaling by Aberrant PI3K in Cancer / regulation of cell shape / actin cytoskeleton / PIP3 activates AKT signaling / protein autophosphorylation / angiogenesis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein-containing complex assembly / cytoplasmic vesicle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / vesicle
Similarity search - Function
Platelet-derived growth factor receptor beta / EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / Platelet-derived growth factor receptor Ig-like domain 4 / : / VEGFR1-3, N-terminal Ig-like domain / PDZ domain 6 / PDZ domain ...Platelet-derived growth factor receptor beta / EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / Platelet-derived growth factor receptor Ig-like domain 4 / : / VEGFR1-3, N-terminal Ig-like domain / PDZ domain 6 / PDZ domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / PDZ domain / Pdz3 Domain / Immunoglobulin domain / PDZ domain / : / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Roll / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Na(+)/H(+) exchange regulatory cofactor NHE-RF1 / Platelet-derived growth factor receptor beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKarthikeyan, S. / Leung, T. / Ladias, J.A.A.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Structural Determinants of the Na+/H+ Exchanger Regulatory Factor Interaction with the Beta 2 Adrenergic and Platelet-Derived Growth Factor Receptors
Authors: Karthikeyan, S. / Leung, T. / Ladias, J.A.A.
#1: 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 Transmembrabe Conductance Regulator
Authors: Karthikeyan, S. / Leung, T. / Ladias, J.A.A.
#2: 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.
History
DepositionNov 20, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EZRIN-RADIXIN-MOESIN BINDING PHOSPHOPROTEIN-50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0193
Polymers9,9481
Non-polymers712
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.073, 50.073, 66.680
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 EZRIN-RADIXIN-MOESIN BINDING PHOSPHOPROTEIN-50 / NA+/H+ EXCHANGER REGULATORY FACTOR


Mass: 9948.382 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) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14745, UniProt: P09619
#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.: 55 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 9-10 ARE CLONING ARTIFACTS. THE AMINO ACID RESIDUES 95-99 OF PDZ1 CORRESPOND TO THE ...RESIDUES 9-10 ARE CLONING ARTIFACTS. THE AMINO ACID RESIDUES 95-99 OF PDZ1 CORRESPOND TO THE CARBOXYL-TERMINAL REGION 1102-1106 OF PDGFR AND SERVE AS A LIGAND FOR A NEIGHBOURING PDZ1 MOLECULE IN THE CRYSTAL.

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growpH: 4.6 / Details: SODIUM ACETATE, SODIUM CHLORIDE, pH 4.60

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 3, 2001 / 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: 2.2→26.4 Å / Num. obs: 4966 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.9 / % possible all: 85.6

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I92

1i92


Resolution: 2.2→26.4 Å / SU B: 8.267 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.234
RfactorNum. reflection% reflectionSelection details
Rfree0.263 268 5.4 %RANDOM
Rwork0.222 ---
obs0.225 4690 99.9 %-
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20.68 Å20 Å2
2--1.37 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms682 0 2 55 739

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