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- PDB-5ndd: Crystal structure of a thermostabilised human protease-activated ... -

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Basic information

Entry
Database: PDB / ID: 5ndd
TitleCrystal structure of a thermostabilised human protease-activated receptor-2 (PAR2) in complex with AZ8838 at 2.8 angstrom resolution
ComponentsLysozyme,Proteinase-activated receptor 2,Soluble cytochrome b562,Proteinase-activated receptor 2
KeywordsMEMBRANE PROTEIN / GPCR / 7TM
Function / homology
Function and homology information


positive regulation of neutrophil mediated killing of gram-negative bacterium / potassium channel activating, G protein-coupled receptor signaling pathway / positive regulation of renin secretion into blood stream / positive regulation of eosinophil degranulation / leukocyte proliferation / mature conventional dendritic cell differentiation / regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of glomerular filtration / negative regulation of toll-like receptor 3 signaling pathway / positive regulation of toll-like receptor 3 signaling pathway ...positive regulation of neutrophil mediated killing of gram-negative bacterium / potassium channel activating, G protein-coupled receptor signaling pathway / positive regulation of renin secretion into blood stream / positive regulation of eosinophil degranulation / leukocyte proliferation / mature conventional dendritic cell differentiation / regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of glomerular filtration / negative regulation of toll-like receptor 3 signaling pathway / positive regulation of toll-like receptor 3 signaling pathway / thrombin-activated receptor activity / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of actin filament depolymerization / cell-cell junction maintenance / positive regulation of cytokine production involved in immune response / positive regulation of toll-like receptor 4 signaling pathway / T cell activation involved in immune response / positive regulation of pseudopodium assembly / negative regulation of chemokine production / positive regulation of phagocytosis, engulfment / positive regulation of chemotaxis / negative regulation of JNK cascade / neutrophil activation / establishment of endothelial barrier / regulation of canonical NF-kappaB signal transduction / positive regulation of positive chemotaxis / positive regulation of leukocyte chemotaxis / positive regulation of Rho protein signal transduction / leukocyte migration / pseudopodium / regulation of blood coagulation / positive regulation of interleukin-10 production / regulation of JNK cascade / G-protein alpha-subunit binding / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of insulin secretion / positive regulation of chemokine production / viral release from host cell by cytolysis / Peptide ligand-binding receptors / peptidoglycan catabolic process / positive regulation of superoxide anion generation / positive regulation of interleukin-1 beta production / electron transport chain / G protein-coupled receptor activity / positive regulation of interleukin-8 production / positive regulation of JNK cascade / positive regulation of GTPase activity / vasodilation / positive regulation of interleukin-6 production / G-protein beta-subunit binding / positive regulation of type II interferon production / blood coagulation / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / signaling receptor activity / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / protease binding / host cell cytoplasm / periplasmic space / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of cell migration / defense response to bacterium / inflammatory response / iron ion binding / G protein-coupled receptor signaling pathway / signaling receptor binding / innate immune response / heme binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
Protease-activated receptor 2 / Protease-activated receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme ...Protease-activated receptor 2 / Protease-activated receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-8TZ / PHOSPHATE ION / Endolysin / Endolysin / Soluble cytochrome b562 / Proteinase-activated receptor 2
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Homo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsCheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. ...Cheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. / Geschwindner, S. / Grebner, C. / Hermansson, N.-O. / Jazayeri, A. / Johansson, P. / Leong, L. / Prihandoko, R. / Rappas, M. / Soutter, H. / Snijder, A. / Sundstrom, L. / Tehan, B. / Thornton, P. / Troast, D. / Wiggin, G. / Zhukov, A. / Marshall, F.H. / Dekker, N.
CitationJournal: Nature / Year: 2017
Title: Structural insight into allosteric modulation of protease-activated receptor 2.
Authors: Cheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G.A. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. / Geschwindner, S. / Grebner, C. / ...Authors: Cheng, R.K.Y. / Fiez-Vandal, C. / Schlenker, O. / Edman, K. / Aggeler, B. / Brown, D.G. / Brown, G.A. / Cooke, R.M. / Dumelin, C.E. / Dore, A.S. / Geschwindner, S. / Grebner, C. / Hermansson, N.O. / Jazayeri, A. / Johansson, P. / Leong, L. / Prihandoko, R. / Rappas, M. / Soutter, H. / Snijder, A. / Sundstrom, L. / Tehan, B. / Thornton, P. / Troast, D. / Wiggin, G. / Zhukov, A. / Marshall, F.H. / Dekker, N.
History
DepositionMar 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme,Proteinase-activated receptor 2,Soluble cytochrome b562,Proteinase-activated receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9114
Polymers69,5591
Non-polymers3523
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-7 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.109, 62.264, 87.341
Angle α, β, γ (deg.)104.88, 90.88, 96.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lysozyme,Proteinase-activated receptor 2,Soluble cytochrome b562,Proteinase-activated receptor 2 / PAR-2 / Coagulation factor II receptor-like 1 / G-protein coupled receptor 11 / Thrombin receptor- ...PAR-2 / Coagulation factor II receptor-like 1 / G-protein coupled receptor 11 / Thrombin receptor-like 1 / Cytochrome b-562 / PAR-2 / Coagulation factor II receptor-like 1 / G-protein coupled receptor 11 / Thrombin receptor-like 1


Mass: 69558.898 Da / Num. of mol.: 1
Mutation: G89A, H108A, G157A, M166L, Y174A, V176E, N222Q, M268A,I289A, L293A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: e, T4Tp126, F2RL1, GPR11, PAR2, cybC / Plasmid: pFASTBAC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: D9IEF7, UniProt: P55085, UniProt: P0ABE7, UniProt: P00720*PLUS, lysozyme
#2: Chemical ChemComp-8TZ / (~{S})-(4-fluoranyl-2-propyl-phenyl)-(1~{H}-imidazol-2-yl)methanol


Mass: 234.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15FN2O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.04 Å3/Da / Density % sol: 59.52 % / Description: Needle-shaped crystals (on average 0.1mm long)
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.8
Details: 0.1 M sodium citrate/citrate acid pH 5.5-6.2, 0.2 M ammonium phosphate dibasic, 38-43 % (w/v) PEG400 and 1 mM AZ8838
PH range: 5.5-6.2 / Temp details: Constant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 2.8→34.34 Å / Num. obs: 17995 / % possible obs: 97.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.11 / Net I/σ(I): 6.5
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2671 / CC1/2: 0.692 / Rpim(I) all: 0.522 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDS2014data reduction
Aimless0.2.17data scaling
PHASER2014phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VW7

3vw7


Resolution: 2.801→34.336 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 30.31
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 858 4.81 %RANDOM
Rwork0.2224 ---
obs0.2244 17823 96.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.801→34.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4498 0 23 10 4531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064624
X-RAY DIFFRACTIONf_angle_d0.6316269
X-RAY DIFFRACTIONf_dihedral_angle_d9.2561664
X-RAY DIFFRACTIONf_chiral_restr0.022726
X-RAY DIFFRACTIONf_plane_restr0.003780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-2.97620.29611390.28112803X-RAY DIFFRACTION96
2.9762-3.20590.31771390.28142842X-RAY DIFFRACTION97
3.2059-3.52820.29021530.25582848X-RAY DIFFRACTION97
3.5282-4.03810.2691520.22612835X-RAY DIFFRACTION97
4.0381-5.08490.25771420.20342830X-RAY DIFFRACTION97
5.0849-34.3390.22161330.18672807X-RAY DIFFRACTION96

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