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- PDB-1gq4: STRUCTURAL DETERMINANTS OF THE NHERF INTERACTION WITH BETA2AR AND... -

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Basic information

Entry
Database: PDB / ID: 1gq4
TitleSTRUCTURAL DETERMINANTS OF THE NHERF INTERACTION WITH BETA2AR AND PDGFR
ComponentsEZRIN-RADIXIN-MOESIN BINDING PHOSPHOPROTEIN-50
KeywordsSIGNALING PROTEIN / PDZ / BETA2-ADRENERGIC RECEPTOR / PDGFR / 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 / positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / negative regulation of smooth muscle contraction / auditory receptor cell stereocilium organization / chloride channel regulator activity / negative regulation of mitotic cell cycle / AMPA selective glutamate receptor signaling pathway / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / norepinephrine binding / Adrenoceptors / beta-2 adrenergic receptor binding / positive regulation of lipophagy / negative regulation of platelet-derived growth factor receptor signaling pathway / growth factor receptor binding / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / nuclear migration / endosome to lysosome transport / response to psychosocial stress / adrenergic receptor signaling pathway / diet induced thermogenesis / regulation of cell size / renal absorption / microvillus membrane / microvillus / positive regulation of cAMP/PKA signal transduction / adenylate cyclase binding / smooth muscle contraction / bone resorption / positive regulation of bone mineralization / potassium channel regulator activity / neuronal dense core vesicle / phosphatase binding / brown fat cell differentiation / transport across blood-brain barrier / intercellular bridge / positive regulation of intrinsic apoptotic signaling pathway / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / protein-membrane adaptor activity / ruffle / sperm midpiece / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endomembrane system / receptor-mediated endocytosis / response to cold / morphogenesis of an epithelium / cell periphery / protein localization to plasma membrane / filopodium / PDZ domain binding / brush border membrane / clathrin-coated endocytic vesicle membrane / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / negative regulation of ERK1 and ERK2 cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Wnt signaling pathway / cellular response to amyloid-beta / mitotic spindle / adenylate cyclase-activating dopamine receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / regulation of cell shape / actin cytoskeleton / Clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / microtubule cytoskeleton / actin cytoskeleton organization / protein-containing complex assembly
Similarity search - Function
EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / Beta 2 adrenoceptor / Adrenoceptor family / PDZ domain / Pdz3 Domain / PDZ domain / Serpentine type 7TM GPCR chemoreceptor Srsx ...EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / : / Beta 2 adrenoceptor / Adrenoceptor family / PDZ domain / Pdz3 Domain / PDZ domain / Serpentine type 7TM GPCR chemoreceptor Srsx / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Roll / Mainly Beta
Similarity search - Domain/homology
Na(+)/H(+) exchange regulatory cofactor NHE-RF1 / Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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.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: 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.A.
History
DepositionNov 19, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 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)9,9845
Polymers9,8421
Non-polymers1424
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.373, 50.373, 66.631
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 / ISOFORM 3 REGULATORY FACTOR 1


Mass: 9842.304 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: P07550
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL MET, RESIDUE 10, IS A CLONING ARTIFACT. THE AMINO ACID RESIDUES 95-99 OF PDZ1 ...THE N-TERMINAL MET, RESIDUE 10, IS A CLONING ARTIFACT. THE AMINO ACID RESIDUES 95-99 OF PDZ1 CORRESPOND TO THE CARBOXYL-TERMINAL REGION 409-413 OF BETA2- ADRENERGIC RECEPTOR 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growpH: 4.24 / Details: CITRIC ACID, LITHIUM CHLORIDE, pH 4.24
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
119 mg/mlprotein1drop
20.1 Mcitric acid1reservoirpH4.24
31 M1reservoirLiCl

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 29, 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: 1.9→26.48 Å / Num. obs: 8091 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 18.73 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 23.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 8.4 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 26.5 Å / Num. obs: 8069 / Num. measured all: 64231
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I92

1i92


Resolution: 1.9→26.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.177 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 372 4.6 %RANDOM
Rwork0.171 ---
obs0.172 7693 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms682 0 4 106 792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021692
X-RAY DIFFRACTIONr_bond_other_d0.0010.02649
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.995935
X-RAY DIFFRACTIONr_angle_other_deg0.70831507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.87389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45915128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2105
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02783
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02127
X-RAY DIFFRACTIONr_nbd_refined0.2320.3122
X-RAY DIFFRACTIONr_nbd_other0.2060.3584
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.566
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0570.51
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.319
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.331
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.521
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1171.5444
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0412706
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.623248
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5454.5229
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 22
Rwork0.203 563
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 26.5 Å / % reflection Rfree: 5 % / Rfactor obs: 0.171 / Rfactor Rfree: 0.186 / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.65

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