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- PDB-4lmm: Crystal structure of NHERF1 PDZ1 domain complexed with the CXCR2 ... -

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Basic information

Entry
Database: PDB / ID: 4lmm
TitleCrystal structure of NHERF1 PDZ1 domain complexed with the CXCR2 C-terminal tail in P21 space group
ComponentsNa(+)/H(+) exchange regulatory cofactor NHE-RF1
KeywordsPROTEIN BINDING / CXCR2 / NHERF1 / Neutrophil / Inflammatory diseases
Function / homology
Function and homology information


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 ...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 / cerebrospinal fluid circulation / negative regulation of sodium ion transport / microvillus assembly / positive regulation of monoatomic ion transmembrane transport / 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 / establishment of Golgi localization / fibroblast migration / type 3 metabotropic glutamate receptor binding / plasma membrane protein complex / 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 / auditory receptor cell stereocilium organization / nuclear migration / regulation of protein kinase activity / beta-2 adrenergic receptor binding / microvillus membrane / regulation of cell size / renal absorption / 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 / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / sperm midpiece / ruffle / filopodium / protein localization to plasma membrane / cell periphery / PDZ domain binding / 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 / 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 / negative regulation of cell population proliferation / signaling receptor binding / protein-containing complex binding / perinuclear region of cytoplasm / extracellular exosome / membrane / identical protein binding / 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 / PDZ superfamily ...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
ACETIC ACID / Na(+)/H(+) exchange regulatory cofactor NHE-RF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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

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Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9563
Polymers9,8601
Non-polymers962
Water2,324129
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


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-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.: 129 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE FIVE RESIDUES MIMIC THE C-TERMINAL TAIL OF CXCR2.

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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, 0.2 M ammonium acetate, 24% PEG4000, pH 4.8, 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: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.1→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: 1.1→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
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JL7

4jl7


Resolution: 1.1→25.89 Å / Cor.coef. Fo:Fc: 0.9561 / Cor.coef. Fo:Fc free: 0.9318 / SU R Cruickshank DPI: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 1503 5.03 %RANDOM
Rwork0.1882 ---
obs0.1897 29864 97.86 %-
all-30517 --
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.0922 Å20 Å2-1.231 Å2
2---0.1969 Å20 Å2
3---0.1047 Å2
Refine analyzeLuzzati coordinate error obs: 0.145 Å
Refinement stepCycle: LAST / Resolution: 1.1→25.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms691 0 5 129 825
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01737HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.161005HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d274SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes20HARMONIC2
X-RAY DIFFRACTIONt_gen_planes115HARMONIC5
X-RAY DIFFRACTIONt_it737HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion4.07
X-RAY DIFFRACTIONt_other_torsion16.31
X-RAY DIFFRACTIONt_chiral_improper_torsion92SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact918SEMIHARMONIC4
LS refinement shellResolution: 1.1→1.14 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2056 116 4.77 %
Rwork0.2071 2318 -
all0.207 2434 -
obs--97.86 %
Refinement TLS params.Method: refined / Origin x: -12.3646 Å / Origin y: -16.3611 Å / Origin z: -23.5356 Å
111213212223313233
T-0.0477 Å20.0063 Å2-0.0064 Å2--0.0359 Å20.0098 Å2---0.0287 Å2
L1.1845 °2-0.3841 °2-0.3953 °2-1.2396 °20.4564 °2--0.6397 °2
S0.0021 Å °0.0515 Å °-0.0465 Å °-0.0039 Å °-0.0617 Å °0.0565 Å °0.0282 Å °-0.0111 Å °0.0595 Å °

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