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- PDB-4p0c: Crystal Structure of NHERF2 PDZ1 Domain in Complex with LPA2 -

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Basic information

Entry
Database: PDB / ID: 4p0c
TitleCrystal Structure of NHERF2 PDZ1 Domain in Complex with LPA2
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF2/Lysophosphatidic acid receptor 2 chimeric protein
KeywordsPROTEIN BINDING / PDZ / protein-protein interaction
Function / homology
Function and homology information


lysophosphatidic acid receptor activity / type 2 metabotropic glutamate receptor binding / Lysosphingolipid and LPA receptors / regulation of metabolic process / type 3 metabotropic glutamate receptor binding / plasma membrane => GO:0005886 / : / phosphatase binding / endomembrane system / protein-membrane adaptor activity ...lysophosphatidic acid receptor activity / type 2 metabotropic glutamate receptor binding / Lysosphingolipid and LPA receptors / regulation of metabolic process / type 3 metabotropic glutamate receptor binding / plasma membrane => GO:0005886 / : / phosphatase binding / endomembrane system / protein-membrane adaptor activity / protein localization to plasma membrane / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / beta-catenin binding / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / protein-containing complex assembly / cadherin binding / apical plasma membrane / G protein-coupled receptor signaling pathway / signaling receptor binding / focal adhesion / lipid binding / cell surface / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Lysophosphatidic acid receptor EDG-4 / Lysophosphatidic acid receptor / EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / PDZ domain / Pdz3 Domain / Serpentine type 7TM GPCR chemoreceptor Srsx / PDZ domain / PDZ domain profile. ...Lysophosphatidic acid receptor EDG-4 / Lysophosphatidic acid receptor / EBP50, C-terminal / Na(+)/H(+) exchange regulatory cofactor NHERF-1/2 / EBP50, C-terminal / PDZ domain / Pdz3 Domain / Serpentine type 7TM GPCR chemoreceptor Srsx / PDZ domain / 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
THIOCYANATE ION / Na(+)/H(+) exchange regulatory cofactor NHE-RF2 / Lysophosphatidic acid receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.339 Å
AuthorsHolcomb, J. / Jiang, Y. / Lu, G. / Trescott, L. / Brunzelle, J. / Sirinupong, N. / Li, C. / Naren, A. / Yang, Z.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Structural insights into PDZ-mediated interaction of NHERF2 and LPA2, a cellular event implicated in CFTR channel regulation.
Authors: Holcomb, J. / Jiang, Y. / Lu, G. / Trescott, L. / Brunzelle, J. / Sirinupong, N. / Li, C. / Naren, A.P. / Yang, Z.
History
DepositionFeb 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.dist
Revision 1.3Mar 27, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF2/Lysophosphatidic acid receptor 2 chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9304
Polymers9,8011
Non-polymers1293
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.360, 40.250, 37.100
Angle α, β, γ (deg.)90.00, 107.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF2/Lysophosphatidic acid receptor 2 chimeric protein


Mass: 9801.165 Da / Num. of mol.: 1
Fragment: UNP Q15599 residues 9-90; UNP Q9HBW0 residues 347-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15599, UniProt: Q9HBW0
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.92 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium acetate, 0.2 M ammonium acetate / PH range: 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.12719 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2013
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12719 Å / Relative weight: 1
ReflectionResolution: 1.17→24.21 Å / Num. obs: 24020 / % possible obs: 95.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 20CS

20cs


Resolution: 1.339→24.208 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1769 841 5.02 %
Rwork0.1449 --
obs0.1466 16738 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.339→24.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms681 0 5 141 827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007711
X-RAY DIFFRACTIONf_angle_d1.191955
X-RAY DIFFRACTIONf_dihedral_angle_d15.408282
X-RAY DIFFRACTIONf_chiral_restr0.069102
X-RAY DIFFRACTIONf_plane_restr0.005131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.339-1.42290.2191450.14142607X-RAY DIFFRACTION100
1.4229-1.53270.18741300.12972651X-RAY DIFFRACTION100
1.5327-1.68690.17191270.12682661X-RAY DIFFRACTION100
1.6869-1.9310.20491350.13462654X-RAY DIFFRACTION100
1.931-2.43240.17681480.14022645X-RAY DIFFRACTION100
2.4324-24.21210.16181560.15942679X-RAY DIFFRACTION99

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