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Yorodumi- PDB-5zkp: Crystal structure of the human platelet-activating factor recepto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zkp | |||||||||
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Title | Crystal structure of the human platelet-activating factor receptor in complex with SR 27417 | |||||||||
Components | Platelet-activating factor receptor,Flavodoxin,Platelet-activating factor receptor | |||||||||
Keywords | SIGNALING 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 / positive regulation of smooth muscle cell proliferation / secretory granule membrane / positive regulation of translation / G protein-coupled receptor activity / lipopolysaccharide binding / phospholipid binding / positive regulation of interleukin-6 production / chemotaxis / Interferon gamma signaling / positive regulation of tumor necrosis factor production / FMN binding / G alpha (q) signalling events / electron transfer activity / inflammatory response / immune response / G protein-coupled receptor signaling pathway / regulation of transcription by RNA polymerase II / Neutrophil degranulation / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Desulfovibrio vulgaris (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | |||||||||
Authors | Cao, C. / Zhao, Q. / Zhang, X.C. / Wu, B. | |||||||||
Funding support | China, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zkp.cif.gz | 193.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zkp.ent.gz | 152.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zkp_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5zkp_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5zkp_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 5zkp_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/5zkp ftp://data.pdbj.org/pub/pdb/validation_reports/zk/5zkp | HTTPS FTP |
-Related structure data
Related structure data | 5zkqC 1f4pS 4xnvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-9ER / |
#3: Chemical | ChemComp-FMN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.54 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: HEPES, PEG 400, NaSCN, Na citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.8→2.95 Å / Rpim(I) all: 0.622 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Displacement parameters | Biso mean: 105.3 Å2
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Refinement step | Cycle: 1 / Resolution: 2.81→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.81→2.98 Å / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 39.1429 Å / Origin y: -10.5284 Å / Origin z: -16.3195 Å
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Refinement TLS group | Selection details: { A|* } |