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- PDB-4q3h: The crystal structure of NHERF1 PDZ2 CXCR2 complex revealed by th... -

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Basic information

Entry
Database: PDB / ID: 4q3h
TitleThe crystal structure of NHERF1 PDZ2 CXCR2 complex revealed by the NHERF1 CXCR2 chimeric protein
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF1
KeywordsIMMUNE SYSTEM / Scaffold protein / Dimerization / Neutrophil chemotaxis
Function / homology
Function and homology information


interleukin-8-mediated signaling pathway / metanephric tubule morphogenesis / negative regulation of neutrophil apoptotic process / interleukin-8 receptor activity / mast cell granule / dopamine receptor binding / import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport ...interleukin-8-mediated signaling pathway / metanephric tubule morphogenesis / negative regulation of neutrophil apoptotic process / interleukin-8 receptor activity / mast cell granule / dopamine receptor binding / import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / interleukin-8 binding / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / positive regulation of monoatomic ion transmembrane transport / C-X-C chemokine receptor activity / acute inflammatory response to antigenic stimulus / bile acid secretion / maintenance of epithelial cell apical/basal polarity / intracellular phosphate ion homeostasis / cilium organization / plasma membrane organization / stereocilium tip / gland morphogenesis / myosin II binding / phospholipase C-activating dopamine receptor signaling pathway / growth factor receptor binding / C-C chemokine receptor activity / neutrophil activation / C-C chemokine binding / establishment of Golgi localization / fibroblast migration / type 3 metabotropic glutamate receptor binding / plasma membrane protein complex / positive regulation of vascular permeability / establishment of epithelial cell apical/basal polarity / negative regulation of fibroblast migration / chloride channel regulator activity / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of neutrophil chemotaxis / auditory receptor cell stereocilium organization / Chemokine receptors bind chemokines / nuclear migration / regulation of protein kinase activity / dendritic cell chemotaxis / beta-2 adrenergic receptor binding / microvillus membrane / regulation of cell size / midbrain development / renal absorption / positive regulation of cardiac muscle cell apoptotic process / microvillus / transport across blood-brain barrier / negative regulation of mitotic cell cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endomembrane system / phosphatase binding / cellular defense response / protein-membrane adaptor activity / positive regulation of intrinsic apoptotic signaling pathway / sperm midpiece / ruffle / neutrophil chemotaxis / secretory granule membrane / filopodium / PDZ domain binding / cell periphery / G protein-coupled receptor activity / calcium-mediated signaling / protein localization to plasma membrane / morphogenesis of an epithelium / brush border membrane / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / receptor internalization / mitotic spindle / beta-catenin binding / Wnt signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / positive regulation of angiogenesis / : / microtubule cytoskeleton / chemotaxis / actin cytoskeleton / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / regulation of cell shape / G alpha (i) signalling events / actin cytoskeleton organization / protein-containing complex assembly / vesicle / transmembrane transporter binding / cell surface receptor signaling pathway / immune response
Similarity search - Function
CXC chemokine receptor 2 / CXC chemokine receptor 1/2 / 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. ...CXC chemokine receptor 2 / CXC chemokine receptor 1/2 / 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 / 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 / C-X-C chemokine receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.443 Å
AuthorsHolcomb, J. / Jiang, Y. / Trescott, L. / Lu, G. / Brunzelle, J. / Sirinupong, N. / Li, C. / Yang, Z.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structure of the NHERF1 PDZ2 domain in complex with the chemokine receptor CXCR2 reveals probable modes of PDZ2 dimerization.
Authors: Holcomb, J. / Jiang, Y. / Guan, X. / Trescott, L. / Lu, G. / Hou, Y. / Wang, S. / Brunzelle, J. / Sirinupong, N. / Li, C. / Yang, Z.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF1


Theoretical massNumber of molelcules
Total (without water)19,8322
Polymers19,8322
Non-polymers00
Water4,486249
1
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF1


Theoretical massNumber of molelcules
Total (without water)9,9161
Polymers9,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Na(+)/H(+) exchange regulatory cofactor NHE-RF1


Theoretical massNumber of molelcules
Total (without water)9,9161
Polymers9,9161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.751, 55.349, 45.226
Angle α, β, γ (deg.)90.00, 90.74, 90.00
Int Tables number4
Space group name H-MP1211

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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: 9916.237 Da / Num. of mol.: 2
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, UniProt: P25025
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris HCl, pH 8.5, 8% PEG8000, 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: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2013
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.443→32.75 Å / Num. all: 28239 / Num. obs: 28239 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 15.43 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.8
Reflection shellResolution: 1.443→1.448 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2302 / % 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 / Resolution: 1.443→32.748 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 1434 5.08 %RANDOM
Rwork0.1654 ---
all0.1669 28233 --
obs0.1669 28233 96.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.443→32.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 0 249 1603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051396
X-RAY DIFFRACTIONf_angle_d1.0531886
X-RAY DIFFRACTIONf_dihedral_angle_d12.028546
X-RAY DIFFRACTIONf_chiral_restr0.055212
X-RAY DIFFRACTIONf_plane_restr0.005254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4428-1.49440.3121010.2542199X-RAY DIFFRACTION78
1.4944-1.55420.26951360.21912620X-RAY DIFFRACTION96
1.5542-1.6250.2461530.20532733X-RAY DIFFRACTION100
1.625-1.71070.22811420.18832760X-RAY DIFFRACTION100
1.7107-1.81780.2021360.1732767X-RAY DIFFRACTION100
1.8178-1.95820.18481430.17062748X-RAY DIFFRACTION100
1.9582-2.15520.1911620.1572747X-RAY DIFFRACTION100
2.1552-2.4670.18411460.16352750X-RAY DIFFRACTION99
2.467-3.10770.19611490.1682737X-RAY DIFFRACTION99
3.1077-32.75670.17771660.14462738X-RAY DIFFRACTION97

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