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- PDB-5tyt: Crystal Structure of the PDZ domain of RhoGEF bound to CXCR2 C-te... -

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Basic information

Entry
Database: PDB / ID: 5tyt
TitleCrystal Structure of the PDZ domain of RhoGEF bound to CXCR2 C-terminal peptide
ComponentsRho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera
KeywordsPROTEIN BINDING / PDZ-RhoGEF / CXCR2
Function / homology
Function and homology information


interleukin-8-mediated signaling pathway / interleukin-8 receptor activity / mast cell granule / interleukin-8 binding / C-X-C chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / neutrophil activation / Sema4D induced cell migration and growth-cone collapse / Chemokine receptors bind chemokines ...interleukin-8-mediated signaling pathway / interleukin-8 receptor activity / mast cell granule / interleukin-8 binding / C-X-C chemokine receptor activity / C-C chemokine receptor activity / C-C chemokine binding / neutrophil activation / Sema4D induced cell migration and growth-cone collapse / Chemokine receptors bind chemokines / regulation of small GTPase mediated signal transduction / dendritic cell chemotaxis / RHOB GTPase cycle / establishment of cell polarity / NRAGE signals death through JNK / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / cellular defense response / striated muscle contraction / RAC1 GTPase cycle / neutrophil chemotaxis / GTPase activator activity / guanyl-nucleotide exchange factor activity / secretory granule membrane / G protein-coupled receptor binding / G protein-coupled receptor activity / regulation of cell growth / calcium-mediated signaling / receptor internalization / mitotic spindle / chemotaxis / microtubule cytoskeleton / G alpha (12/13) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / actin cytoskeleton organization / cell surface receptor signaling pathway / inflammatory response / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of DNA-templated transcription / cell surface / signal transduction / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CXC chemokine receptor 2 / Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / CXC chemokine receptor 1/2 / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / ARHGEF1-like, PH domain / PH domain / RGS, subdomain 2 / RGS domain ...CXC chemokine receptor 2 / Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / CXC chemokine receptor 1/2 / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / ARHGEF1-like, PH domain / PH domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / PDZ domain / Pdz3 Domain / PH domain profile. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology 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) / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 11 / C-X-C chemokine receptor type 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsSpellmon, N. / Holcomb, J. / Niu, A. / Choudhary, V. / Sun, X. / Brunzelle, J. / Li, C. / Yang, Z.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural basis of PDZ-mediated chemokine receptor CXCR2 scaffolding by guanine nucleotide exchange factor PDZ-RhoGEF.
Authors: Spellmon, N. / Holcomb, J. / Niu, A. / Choudhary, V. / Sun, X. / Zhang, Y. / Wan, J. / Doughan, M. / Hayden, S. / Hachem, F. / Brunzelle, J. / Li, C. / Yang, Z.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.detector / _software.classification
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera
B: Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera
C: Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera
D: Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera


Theoretical massNumber of molelcules
Total (without water)37,4244
Polymers37,4244
Non-polymers00
Water23413
1
A: Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera
B: Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera


Theoretical massNumber of molelcules
Total (without water)18,7122
Polymers18,7122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera

D: Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera


Theoretical massNumber of molelcules
Total (without water)18,7122
Polymers18,7122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)61.739, 66.633, 168.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Rho guanine nucleotide exchange factor 11, C-X-C chemokine receptor type 2 chimera / PDZ-RhoGEF / CXCR-2 / CDw128b / GRO/MGSA receptor / High affinity interleukin-8 receptor B / IL-8R ...PDZ-RhoGEF / CXCR-2 / CDw128b / GRO/MGSA receptor / High affinity interleukin-8 receptor B / IL-8R B / IL-8 receptor type 2


Mass: 9355.930 Da / Num. of mol.: 4
Fragment: Rho (UNP residues 41-123), CXCR2 C-terminal peptide (UNP residues 356-360)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF11, KIAA0380, CXCR2, IL8RB / Plasmid: pCDF-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15085, UniProt: P25025
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.31 Å3/Da / Density % sol: 46.86 % / Description: diamond-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG8000, 0.1 M sodium citrate, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07822 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 14, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07822 Å / Relative weight: 1
ReflectionResolution: 2.398→84.22 Å / Num. obs: 13997 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.2
Reflection shellResolution: 2.398→2.439 Å / Rmerge(I) obs: 0.738

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
autoPROCdata scaling
XDSdata reduction
Aimless0.5.28data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5E6P

5e6p


Resolution: 2.398→43.734 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 694 4.97 %
Rwork0.2065 13259 -
obs0.2081 13953 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.64 Å2 / Biso mean: 64.8974 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.398→43.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 0 13 2610
Biso mean---51.51 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112629
X-RAY DIFFRACTIONf_angle_d1.2743539
X-RAY DIFFRACTIONf_chiral_restr0.056446
X-RAY DIFFRACTIONf_plane_restr0.004441
X-RAY DIFFRACTIONf_dihedral_angle_d13.515963
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3976-2.58270.35331450.30262574271999
2.5827-2.84260.33021480.281426142762100
2.8426-3.25380.31321230.248626582781100
3.2538-4.0990.271570.207426442801100
4.099-43.74160.16591210.16822769289099

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