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- PDB-4pqw: Crystal Structure of Phospholipase C beta 3 in Complex with PDZ1 ... -

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Basic information

Entry
Database: PDB / ID: 4pqw
TitleCrystal Structure of Phospholipase C beta 3 in Complex with PDZ1 of NHERF1
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF1
KeywordsPROTEIN BINDING / NHERF1 / PLCb3 / Scaffold protein / Pancreatic cancer
Function / homology
Function and homology information


regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / renal phosphate ion absorption / import across plasma membrane / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / cerebrospinal fluid circulation ...regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / renal phosphate ion absorption / import across plasma membrane / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / maintenance of epithelial cell apical/basal polarity / bile acid secretion / positive regulation of monoatomic ion transmembrane transport / regulation of protein kinase activity / channel activator activity / stereocilium tip / phospholipase C-activating dopamine receptor signaling pathway / plasma membrane organization / cilium organization / gland morphogenesis / myosin II binding / growth factor receptor binding / establishment of Golgi localization / intracellular phosphate ion homeostasis / fibroblast migration / type 3 metabotropic glutamate receptor binding / plasma membrane protein complex / establishment of epithelial cell apical/basal polarity / negative regulation of fibroblast migration / auditory receptor cell stereocilium organization / chloride channel regulator activity / negative regulation of platelet-derived growth factor receptor signaling pathway / beta-2 adrenergic receptor binding / nuclear migration / microvillus membrane / regulation of cell size / renal absorption / microvillus / negative regulation of mitotic cell cycle / phosphatase binding / transport across blood-brain barrier / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / ruffle / sperm midpiece / endomembrane system / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein localization to plasma membrane / morphogenesis of an epithelium / cell periphery / PDZ domain binding / filopodium / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / brush border membrane / 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 / signaling receptor binding / negative regulation of cell population proliferation / protein-containing complex binding / 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
NICKEL (II) ION / Na(+)/H(+) exchange regulatory cofactor NHE-RF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsJiang, Y. / Wang, S. / Holcomb, J. / Trescott, L. / Guan, X. / Hou, Y. / Brunzelle, J. / Sirinupong, N. / Li, C. / Yang, Z.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystallographic analysis of NHERF1-PLC beta 3 interaction provides structural basis for CXCR2 signaling in pancreatic cancer.
Authors: Jiang, Y. / Wang, S. / Holcomb, J. / Trescott, L. / Guan, X. / Hou, Y. / Brunzelle, J. / Sirinupong, N. / Li, C. / Yang, Z.
History
DepositionMar 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 cofactor NHE-RF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1436
Polymers9,9421
Non-polymers2015
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.660, 50.660, 66.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

21A-343-

HOH

31A-373-

HOH

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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: 9942.378 Da / Num. of mol.: 1 / Fragment: unp residues 11-94
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHERF, NHERF1, SLC9A3R1 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14745
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium acetate, pH 4.6, 2.5 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.1272 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2013
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.47→33.3 Å / Num. all: 17247 / Num. obs: 17247 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 21.2
Reflection shellResolution: 1.47→1.51 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4JL7

4jl7


Resolution: 1.47→26.545 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 870 5.07 %Random
Rwork0.1794 ---
obs0.1802 17175 99.08 %-
all-17247 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→26.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms697 0 5 93 795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005712
X-RAY DIFFRACTIONf_angle_d0.954963
X-RAY DIFFRACTIONf_dihedral_angle_d13.865277
X-RAY DIFFRACTIONf_chiral_restr0.05108
X-RAY DIFFRACTIONf_plane_restr0.004130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.56210.31081470.2572648X-RAY DIFFRACTION99
1.5621-1.68270.28081470.21182701X-RAY DIFFRACTION99
1.6827-1.8520.23811590.17982677X-RAY DIFFRACTION100
1.852-2.11990.18881350.16592731X-RAY DIFFRACTION100
2.1199-2.67040.20131580.17242747X-RAY DIFFRACTION100
2.6704-26.54930.16871240.17682801X-RAY DIFFRACTION97

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