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- PDB-4n6x: Crystal Structure of the Chemokine Receptor CXCR2 in Complex with... -

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Basic information

Entry
Database: PDB / ID: 4n6x
TitleCrystal Structure of the Chemokine Receptor CXCR2 in Complex with the First PDZ Domain of NHERF1
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF1/Chemokine Receptor CXCR2 fusion protein
KeywordsSIGNALING PROTEIN / CXCR2 / NHERF1 / Neutrophil / inflammatory diseases
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
Na(+)/H(+) exchange regulatory cofactor NHE-RF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.051 Å
AuthorsLu, G. / Wu, Y. / Jiang, Y. / Brunzelle, J. / Sirinupong, N. / Li, C. / Yang, Z.
CitationJournal: Plos One / Year: 2013
Title: New Conformational State of NHERF1-CXCR2 Signaling Complex Captured by Crystal Lattice Trapping.
Authors: Jiang, Y. / Lu, G. / Trescott, L.R. / Hou, Y. / Guan, X. / Wang, S. / Stamenkovich, A. / Brunzelle, J. / Sirinupong, N. / Li, C. / Yang, Z.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 cofactor NHE-RF1/Chemokine Receptor CXCR2 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0025
Polymers9,8601
Non-polymers1424
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.380, 50.380, 65.940
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-286-

HOH

21A-301-

HOH

31A-302-

HOH

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Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF1/Chemokine Receptor CXCR2 fusion protein / 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: 9860.318 Da / Num. of mol.: 1 / Fragment: First PDZ Domain (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE 5 C-TERMINAL RESIDUES ARE FROM CHEMOKINE RECEPTOR CXCR2 FUSED TO THE PDZ DOMAIN OF NHERF1 ...THE 5 C-TERMINAL RESIDUES ARE FROM CHEMOKINE RECEPTOR CXCR2 FUSED TO THE PDZ DOMAIN OF NHERF1 DURING CLONING TO MIMIC THE INTERACTION AND FACILITATE NHERF1-CXCR2 COCRYSTALLIZATION.

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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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium acetate, pH 4.6, 2.7 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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2013
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.05→36.39 Å / Num. obs: 45541 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 23.3
Reflection shellResolution: 1.05→1.08 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3264 / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.051→26.304 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 13.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1634 2297 5.05 %RANDOM
Rwork0.1476 ---
obs0.1484 45494 99.63 %-
all-45494 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.1 Å2
Refinement stepCycle: LAST / Resolution: 1.051→26.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms691 0 4 105 800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007738
X-RAY DIFFRACTIONf_angle_d1.1621002
X-RAY DIFFRACTIONf_dihedral_angle_d14.639287
X-RAY DIFFRACTIONf_chiral_restr0.06112
X-RAY DIFFRACTIONf_plane_restr0.005136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0506-1.07340.25951330.22942589X-RAY DIFFRACTION97
1.0734-1.09840.18781500.17072648X-RAY DIFFRACTION100
1.0984-1.12580.16621480.15592667X-RAY DIFFRACTION100
1.1258-1.15630.15931360.13792668X-RAY DIFFRACTION100
1.1563-1.19030.14951420.13312654X-RAY DIFFRACTION100
1.1903-1.22870.12681360.12362709X-RAY DIFFRACTION100
1.2287-1.27260.15471530.11722646X-RAY DIFFRACTION100
1.2726-1.32360.12291640.1092694X-RAY DIFFRACTION100
1.3236-1.38380.11651350.11012707X-RAY DIFFRACTION100
1.3838-1.45680.12311260.10812697X-RAY DIFFRACTION100
1.4568-1.5480.12671480.10742694X-RAY DIFFRACTION100
1.548-1.66760.11421430.10712712X-RAY DIFFRACTION100
1.6676-1.83530.11781470.11552720X-RAY DIFFRACTION100
1.8353-2.10080.13581440.12712734X-RAY DIFFRACTION100
2.1008-2.64640.15521370.15082789X-RAY DIFFRACTION100
2.6464-26.31250.21381550.18512869X-RAY DIFFRACTION99

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