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- PDB-4mpa: Crystal structure of NHERF1-CXCR2 signaling complex in P21 space group -

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Basic information

Entry
Database: PDB / ID: 4mpa
TitleCrystal structure of NHERF1-CXCR2 signaling complex in P21 space group
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF1, C-X-C chemokine receptor type 2 chimera
KeywordsSTRUCTURAL PROTEIN / neutrophil / inflammatory diseases
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 / import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding ...interleukin-8-mediated signaling pathway / metanephric tubule morphogenesis / negative regulation of neutrophil apoptotic process / interleukin-8 receptor activity / mast cell granule / import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / 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 / plasma membrane organization / stereocilium tip / cilium organization / intracellular phosphate ion homeostasis / gland morphogenesis / myosin II binding / phospholipase C-activating dopamine receptor signaling pathway / growth factor receptor binding / C-C chemokine receptor activity / establishment of Golgi localization / C-C chemokine binding / fibroblast migration / type 3 metabotropic glutamate receptor binding / plasma membrane protein complex / neutrophil activation / 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 / phosphatase binding / endomembrane system / cellular defense response / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / sperm midpiece / ruffle / neutrophil chemotaxis / secretory granule membrane / filopodium / protein localization to plasma membrane / G protein-coupled receptor activity / cell periphery / calcium-mediated signaling / PDZ domain binding / morphogenesis of an epithelium / brush border membrane / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / receptor internalization / negative regulation of ERK1 and ERK2 cascade / mitotic spindle / beta-catenin binding / Wnt signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / positive regulation of angiogenesis / : / chemotaxis / microtubule cytoskeleton / actin cytoskeleton / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of cell shape / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / protein-containing complex assembly / vesicle / transmembrane transporter binding / cell surface receptor signaling pathway / inflammatory 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
ACETIC ACID / 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: 1.097 Å
AuthorsJiang, Y. / Lu, G. / Wu, 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
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: struct_ref / struct_ref_seq
Item: _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
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 / 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

Downloads & links

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Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF1, C-X-C chemokine receptor type 2 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9563
Polymers9,8601
Non-polymers962
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.593, 45.509, 33.446
Angle α, β, γ (deg.)90.00, 109.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF1, C-X-C chemokine receptor type 2 chimera / 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 / CXC-R2 / CXCR-2 / CDw128b / GRO/MGSA receptor / High affinity interleukin-8 receptor B / IL-8R B / L-8 receptor type 2


Mass: 9860.318 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHERF, NHERF1, SLC9A3R1, CXCR2 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14745, UniProt: P25025
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN IS A CHIMERA OF RESIDUES 11-95 OF PDZ DOMAIN OF NHERF1 AND RESIDUES 356-360 OF CXCR2 ...PROTEIN IS A CHIMERA OF RESIDUES 11-95 OF PDZ DOMAIN OF NHERF1 AND RESIDUES 356-360 OF CXCR2 (RESIDUE 95 OF NHERF1 AND RESIDUE 356 OF CXCR2 ARE THE SAME RESIDUE).

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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: 1.93 Å3/Da / Density % sol: 36.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 100 mM sodium acetate, pH 4.8, 0.2 M ammonium acetate, 24% PEG4000, 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 4, 2013
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.097→45.5 Å / Num. all: 30032 / Num. obs: 30032 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 8.17 Å2 / Rmerge(I) obs: 0.024 / Net I/σ(I): 24.8
Reflection shellResolution: 1.097→1.16 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3845 / % possible all: 86

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JL7

4jl7


Resolution: 1.097→25.893 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1569 1508 5.03 %RANDOM
Rwork0.1434 ---
obs0.1441 30006 97.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.097→25.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms691 0 5 158 854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01731
X-RAY DIFFRACTIONf_angle_d1.425995
X-RAY DIFFRACTIONf_dihedral_angle_d13.239288
X-RAY DIFFRACTIONf_chiral_restr0.065115
X-RAY DIFFRACTIONf_plane_restr0.005133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.097-1.13290.19281050.1582101X-RAY DIFFRACTION80
1.1329-1.17330.16221290.1382593X-RAY DIFFRACTION97
1.1733-1.22030.15691300.12372635X-RAY DIFFRACTION100
1.2203-1.27590.13541260.11932653X-RAY DIFFRACTION100
1.2759-1.34310.13881580.11772641X-RAY DIFFRACTION100
1.3431-1.42730.14031370.11962611X-RAY DIFFRACTION100
1.4273-1.53750.1281300.122671X-RAY DIFFRACTION100
1.5375-1.69210.1461410.12412669X-RAY DIFFRACTION100
1.6921-1.93690.15831490.13562638X-RAY DIFFRACTION100
1.9369-2.440.1611500.14432653X-RAY DIFFRACTION100
2.44-25.90010.16721530.16912633X-RAY DIFFRACTION97

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