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

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Basic information

Entry
Database: PDB / ID: 5zkp
TitleCrystal structure of the human platelet-activating factor receptor in complex with SR 27417
ComponentsPlatelet-activating factor receptor,Flavodoxin,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 sensory perception of pain / 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 ...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 sensory perception of pain / 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 / lipopolysaccharide immune receptor activity / response to symbiotic bacterium / positive regulation of neutrophil degranulation / parturition / positive regulation of voltage-gated chloride channel activity / 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 / phosphatidylinositol-mediated signaling / tertiary granule membrane / : / cellular response to cAMP / negative regulation of blood pressure / 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 / positive regulation of tumor necrosis factor production / Interferon gamma signaling / FMN binding / G alpha (q) signalling events / electron transfer activity / 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 / Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / G-protein coupled receptors family 1 signature. ...Platelet-activating factor receptor / Flavodoxin, short chain / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin-like / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like 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)
Similarity search - Domain/homology
Chem-9ER / FLAVIN MONONUCLEOTIDE / Flavodoxin / Platelet-activating factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Desulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,3523
Polymers52,4301
Non-polymers9212
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-7 kcal/mol
Surface area21740 Å2
Unit cell
Length a, b, c (Å)67.050, 67.050, 280.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Platelet-activating factor receptor,Flavodoxin,Platelet-activating factor receptor / PAFr / PAFr


Mass: 52430.477 Da / Num. of mol.: 1 / Mutation: F116Y, N169D,P2A, Y98W,A230D, V234A, D289N
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Platelet-activating factor receptor (UNP residues 2-216), Flavodoxin (UNP residues 2-148), Platelet-activating factor receptor (UNP residues 224-316), and tags
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Desulfovibrio vulgaris (bacteria)
Gene: PTAFR, PAFR, DVU_2680 / Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25105, UniProt: P00323
#2: Chemical ChemComp-9ER / N1,N1-dimethyl-N2-[(pyridin-3-yl)methyl]-N2-{4-[2,4,6-tri(propan-2-yl)phenyl]-1,3-thiazol-2-yl}ethane-1,2-diamine


Mass: 464.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H40N4S
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P

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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: 3.47 Å3/Da / Density % sol: 64.54 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: HEPES, PEG 400, NaSCN, Na citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 18902 / % possible obs: 99.4 % / Redundancy: 7.6 % / Biso Wilson estimate: 78.45 Å2 / Rpim(I) all: 0.087 / Net I/σ(I): 16.9
Reflection shellResolution: 2.8→2.95 Å / Rpim(I) all: 0.622

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XNV, 1F4P

4xnv

1f4p


Resolution: 2.81→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.617 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.628 / SU Rfree Blow DPI: 0.326 / SU Rfree Cruickshank DPI: 0.33
RfactorNum. reflection% reflectionSelection details
Rfree0.259 887 5.07 %RANDOM
Rwork0.222 ---
obs0.224 17489 93.5 %-
Displacement parametersBiso mean: 105.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.1151 Å20 Å20 Å2
2--2.1151 Å20 Å2
3----4.2302 Å2
Refinement stepCycle: 1 / Resolution: 2.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 64 0 3450
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013546HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084844HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1143SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes524HARMONIC5
X-RAY DIFFRACTIONt_it3546HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.41
X-RAY DIFFRACTIONt_other_torsion21.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion469SEMIHARMONIC5
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_contact4129SEMIHARMONIC4
LS refinement shellResolution: 2.81→2.98 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.295 -4.72 %
Rwork0.2271 1756 -
all0.2303 1843 -
obs--62.88 %
Refinement TLS params.Method: refined / Origin x: 39.1429 Å / Origin y: -10.5284 Å / Origin z: -16.3195 Å
111213212223313233
T0.0161 Å2-0.3182 Å2-0.022 Å2-0.0325 Å2-0.0042 Å2---0.304 Å2
L0.4856 °2-0.1872 °2-0.6358 °2-2.3774 °22.0032 °2--6.0666 °2
S0.3252 Å °0.0616 Å °-0.0851 Å °0.1469 Å °-0.4022 Å °-0.1049 Å °0.0147 Å °0.4768 Å °0.077 Å °
Refinement TLS groupSelection details: { A|* }

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