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- PDB-4jl7: Crystal Structure of the Chemokine Receptor CXCR2 in Complex with... -

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Basic information

Entry
Database: PDB / ID: 4jl7
TitleCrystal Structure of the Chemokine Receptor CXCR2 in Complex with the First PDZ Domain of NHERF1
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF1
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: 1.16 Å
AuthorsLu, G. / Wu, Y. / Jiang, Y. / Brunzelle, J. / Sirinupong, N. / Li, C. / Yang, Z.
CitationJournal: Plos One / Year: 2013
Title: Structural Insights into Neutrophilic Migration Revealed by the Crystal Structure of the Chemokine Receptor CXCR2 in Complex with the First PDZ Domain of NHERF1.
Authors: Lu, G. / Wu, Y. / Jiang, Y. / Wang, S. / Hou, Y. / Guan, X. / Brunzelle, J. / Sirinupong, N. / Sheng, S. / Li, C. / Yang, Z.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9674
Polymers9,8601
Non-polymers1063
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.360, 50.360, 65.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsone molecule per asymmetric unit

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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: 9860.318 Da / Num. of mol.: 1 / Fragment: unp residues 11-95
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.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium acetate, 2.7 M sodium chloride, pH 4.6, 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: 1.16→20 Å / Num. all: 33912 / Num. obs: 33912 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 11.75 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 19.1
Reflection shellResolution: 1.16→1.23 Å / Redundancy: 7 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.3 / Num. unique all: 4891 / Rsym value: 0.463 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→20 Å / Cor.coef. Fo:Fc: 0.9575 / Cor.coef. Fo:Fc free: 0.9422 / SU R Cruickshank DPI: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2083 1717 5.07 %RANDOM
Rwork0.1861 ---
all0.1872 34079 --
obs0.1872 33875 99.4 %-
Displacement parametersBiso mean: 21.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.8391 Å20 Å20 Å2
2---1.8391 Å20 Å2
3---3.6783 Å2
Refine analyzeLuzzati coordinate error obs: 0.155 Å
Refinement stepCycle: LAST / Resolution: 1.16→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms691 0 3 99 793
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011701HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.23947HARMONIC2
X-RAY DIFFRACTIONt_trig_c_planes19HARMONIC2
X-RAY DIFFRACTIONt_gen_planes102HARMONIC5
X-RAY DIFFRACTIONt_it701HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion86SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact843SEMIHARMONIC4
LS refinement shellResolution: 1.16→1.2 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2482 126 4.64 %
Rwork0.217 2588 -
all0.2184 2714 -
obs--99.4 %
Refinement TLS params.Method: refined / Origin x: 32.1655 Å / Origin y: 15.6379 Å / Origin z: 1.3801 Å
111213212223313233
T-0.0085 Å2-0.0042 Å20.0077 Å2--0.0136 Å2-0.0037 Å2---0.0232 Å2
L0.7385 °20.5953 °2-0.5142 °2-1.0368 °2-0.0561 °2--1.4352 °2
S-0.0049 Å °-0.0889 Å °-0.0516 Å °-0.0871 Å °-0.0368 Å °-0.0464 Å °0.0656 Å °0.0722 Å °0.0417 Å °
Refinement TLS groupSelection details: { A|9 - A|99 }

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