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- PDB-5zkq: Crystal structure of the human platelet-activating factor recepto... -

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Basic information

Entry
Database: PDB / ID: 5zkq
TitleCrystal structure of the human platelet-activating factor receptor in complex with ABT-491
ComponentsPlatelet-activating factor receptor,Endolysin,Endolysin,Platelet-activating factor receptor
KeywordsSIGNALING PROTEIN / G protein-coupled receptor / Platelet-activating factor receptor / Complex
Function / homology
Function and homology information


cellular response to gravity / positive regulation of maternal process involved in parturition / cellular response to 2-O-acetyl-1-O-hexadecyl-sn-glycero-3-phosphocholine / positive regulation of gastro-intestinal system smooth muscle contraction / positive regulation of transcytosis / platelet activating factor receptor activity / inositol trisphosphate biosynthetic process / positive regulation of cellular extravasation / G protein-coupled purinergic nucleotide receptor activity / response to symbiotic bacterium ...cellular response to gravity / positive regulation of maternal process involved in parturition / cellular response to 2-O-acetyl-1-O-hexadecyl-sn-glycero-3-phosphocholine / positive regulation of gastro-intestinal system smooth muscle contraction / positive regulation of transcytosis / platelet activating factor receptor activity / inositol trisphosphate biosynthetic process / positive regulation of cellular extravasation / G protein-coupled purinergic nucleotide receptor activity / response to symbiotic bacterium / positive regulation of neutrophil degranulation / lipopolysaccharide immune receptor activity / parturition / positive regulation of leukocyte tethering or rolling / Class A/1 (Rhodopsin-like receptors) / transcytosis / mitogen-activated protein kinase binding / cellular response to fatty acid / positive regulation of inositol phosphate biosynthetic process / response to dexamethasone / Interleukin-10 signaling / tertiary granule membrane / viral release from host cell by cytolysis / cellular response to cAMP / negative regulation of blood pressure / peptidoglycan catabolic process / secretory granule membrane / positive regulation of translation / G protein-coupled receptor activity / lipopolysaccharide binding / positive regulation of smooth muscle cell proliferation / phospholipid binding / positive regulation of interleukin-6 production / chemotaxis / Interferon gamma signaling / positive regulation of tumor necrosis factor production / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / host cell cytoplasm / defense response to bacterium / inflammatory response / immune response / G protein-coupled receptor signaling pathway / Neutrophil degranulation / regulation of transcription by RNA polymerase II / membrane / plasma membrane
Similarity search - Function
Platelet-activating factor receptor / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM ...Platelet-activating factor receptor / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-9EU / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Endolysin / Platelet-activating factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCao, C. / Zhao, Q. / Zhang, X.C. / Wu, B.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)81525024 China
Ministry of Education (China)B08029 China
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural basis for signal recognition and transduction by platelet-activating-factor receptor.
Authors: Cao, C. / Tan, Q. / Xu, C. / He, L. / Yang, L. / Zhou, Y. / Zhou, Y. / Qiao, A. / Lu, M. / Yi, C. / Han, G.W. / Wang, X. / Li, X. / Yang, H. / Rao, Z. / Jiang, H. / Zhao, Y. / Liu, J. / ...Authors: Cao, C. / Tan, Q. / Xu, C. / He, L. / Yang, L. / Zhou, Y. / Zhou, Y. / Qiao, A. / Lu, M. / Yi, C. / Han, G.W. / Wang, X. / Li, X. / Yang, H. / Rao, Z. / Jiang, H. / Zhao, Y. / Liu, J. / Stevens, R.C. / Zhao, Q. / Zhang, X.C. / Wu, B.
History
DepositionMar 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Platelet-activating factor receptor,Endolysin,Endolysin,Platelet-activating factor receptor
B: Platelet-activating factor receptor,Endolysin,Endolysin,Platelet-activating factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,41719
Polymers100,2552
Non-polymers4,16217
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-116 kcal/mol
Surface area30730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.220, 166.540, 100.310
Angle α, β, γ (deg.)90.00, 100.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Platelet-activating factor receptor,Endolysin,Endolysin,Platelet-activating factor receptor / PAFr / Lysis protein / Lysozyme / Muramidase


Mass: 50127.543 Da / Num. of mol.: 2
Mutation: F116Y, N169D, A230D,C97A, I137R, A230D, V234A, D289N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: PTAFR, PAFR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25105, UniProt: P00720, lysozyme

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Non-polymers , 5 types, 19 molecules

#2: Chemical ChemComp-9EU / 4-ethynyl-3-{3-fluoro-4-[(2-methyl-1H-imidazo[4,5-c]pyridin-1-yl)methyl]benzene-1-carbonyl}-N,N-dimethyl-1H-indole-1-carboxamide


Mass: 479.505 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H22FN5O2
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.54 Å3/Da / Density % sol: 65.23 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: HEPES, PEG 400, MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 30671 / % possible obs: 98.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 91.8 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 5.7
Reflection shellResolution: 2.9→3.06 Å / Rmerge(I) obs: 0.91

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U15

4u15


Resolution: 2.9→49.39 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.479 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.426 / SU Rfree Blow DPI: 0.277 / SU Rfree Cruickshank DPI: 0.29
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1507 4.91 %RANDOM
Rwork0.203 ---
obs0.204 30664 99.3 %-
Displacement parametersBiso mean: 85.97 Å2
Baniso -1Baniso -2Baniso -3
1--21.6581 Å20 Å2-10.4198 Å2
2--21.5973 Å20 Å2
3---0.0608 Å2
Refinement stepCycle: 1 / Resolution: 2.9→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5309 0 249 2 5560
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015699HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.117757HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1856SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes829HARMONIC5
X-RAY DIFFRACTIONt_it5699HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion20.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion752SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6884SEMIHARMONIC4
LS refinement shellResolution: 2.9→3 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2855 165 5.47 %
Rwork0.2211 2852 -
all0.2247 3017 -
obs--99.38 %

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