5zkq

From Proteopedia

(Difference between revisions)

Revision as of 08:59, 22 November 2023

Crystal structure of the human platelet-activating factor receptor in complex with ABT-491

Structural highlights

5zkq is a 2 chain structure with sequence from Escherichia virus T4 and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PTAFR_HUMAN Receptor for platelet activating factor, a chemotactic phospholipid mediator that possesses potent inflammatory, smooth-muscle contractile and hypotensive activity. Seems to mediate its action via a G protein that activates a phosphatidylinositol-calcium second messenger system.^[1] ^[2] ^[3] ^[4] ENLYS_BPT4 Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.^[5]

Publication Abstract from PubMed

Platelet-activating-factor receptor (PAFR) responds to platelet-activating factor (PAF), a phospholipid mediator of cell-to-cell communication that exhibits diverse physiological effects. PAFR is considered an important drug target for treating asthma, inflammation and cardiovascular diseases. Here we report crystal structures of human PAFR in complex with the antagonist SR 27417 and the inverse agonist ABT-491 at 2.8-A and 2.9-A resolution, respectively. The structures, supported by molecular docking of PAF, provide insights into the signal-recognition mechanisms of PAFR. The PAFR-SR 27417 structure reveals an unusual conformation showing that the intracellular tips of helices II and IV shift outward by 13 A and 4 A, respectively, and helix VIII adopts an inward conformation. The PAFR structures, combined with single-molecule FRET and cell-based functional assays, suggest that the conformational change in the helical bundle is ligand dependent and plays a critical role in PAFR activation, thus greatly extending knowledge about signaling by G-protein-coupled receptors.

Structural basis for signal recognition and transduction by platelet-activating-factor receptor.,Cao C, Tan Q, Xu C, He L, Yang L, Zhou Y, Zhou Y, Qiao A, Lu M, Yi C, Han GW, Wang X, Li X, Yang H, Rao Z, Jiang H, Zhao Y, Liu J, Stevens RC, Zhao Q, Zhang XC, Wu B Nat Struct Mol Biol. 2018 Jun;25(6):488-495. doi: 10.1038/s41594-018-0068-y. Epub, 2018 May 28. PMID:29808000^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sugimoto T, Tsuchimochi H, McGregor CG, Mutoh H, Shimizu T, Kurachi Y. Molecular cloning and characterization of the platelet-activating factor receptor gene expressed in the human heart. Biochem Biophys Res Commun. 1992 Dec 15;189(2):617-24. PMID:1281995
↑ Kunz D, Gerard NP, Gerard C. The human leukocyte platelet-activating factor receptor. cDNA cloning, cell surface expression, and construction of a novel epitope-bearing analog. J Biol Chem. 1992 May 5;267(13):9101-6. PMID:1374385
↑ Ye RD, Prossnitz ER, Zou AH, Cochrane CG. Characterization of a human cDNA that encodes a functional receptor for platelet activating factor. Biochem Biophys Res Commun. 1991 Oct 15;180(1):105-11. PMID:1656963
↑ Nakamura M, Honda Z, Izumi T, Sakanaka C, Mutoh H, Minami M, Bito H, Seyama Y, Matsumoto T, Noma M, et al.. Molecular cloning and expression of platelet-activating factor receptor from human leukocytes. J Biol Chem. 1991 Oct 25;266(30):20400-5. PMID:1657923
↑ Moussa SH, Kuznetsov V, Tran TA, Sacchettini JC, Young R. Protein determinants of phage T4 lysis inhibition. Protein Sci. 2012 Apr;21(4):571-82. doi: 10.1002/pro.2042. Epub 2012 Mar 2. PMID:22389108 doi:http://dx.doi.org/10.1002/pro.2042
↑ Cao C, Tan Q, Xu C, He L, Yang L, Zhou Y, Zhou Y, Qiao A, Lu M, Yi C, Han GW, Wang X, Li X, Yang H, Rao Z, Jiang H, Zhao Y, Liu J, Stevens RC, Zhao Q, Zhang XC, Wu B. Structural basis for signal recognition and transduction by platelet-activating-factor receptor. Nat Struct Mol Biol. 2018 Jun;25(6):488-495. doi: 10.1038/s41594-018-0068-y. Epub, 2018 May 28. PMID:29808000 doi:http://dx.doi.org/10.1038/s41594-018-0068-y

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5zkq"

@@ Line 3: / Line 3: @@
 <StructureSection load='5zkq' size='340' side='right'caption='[[5zkq]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5zkq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZKQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5zkq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZKQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=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'>9EU</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=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'>9EU</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkq OCA], [http://pdbe.org/5zkq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zkq RCSB], [http://www.ebi.ac.uk/pdbsum/5zkq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkq ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5zkq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zkq OCA], [https://pdbe.org/5zkq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zkq RCSB], [https://www.ebi.ac.uk/pdbsum/5zkq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zkq ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PTAFR_HUMAN PTAFR_HUMAN]] Receptor for platelet activating factor, a chemotactic phospholipid mediator that possesses potent inflammatory, smooth-muscle contractile and hypotensive activity. Seems to mediate its action via a G protein that activates a phosphatidylinositol-calcium second messenger system.<ref>PMID:1281995</ref> <ref>PMID:1374385</ref> <ref>PMID:1656963</ref> <ref>PMID:1657923</ref>
+[https://www.uniprot.org/uniprot/PTAFR_HUMAN PTAFR_HUMAN] Receptor for platelet activating factor, a chemotactic phospholipid mediator that possesses potent inflammatory, smooth-muscle contractile and hypotensive activity. Seems to mediate its action via a G protein that activates a phosphatidylinositol-calcium second messenger system.<ref>PMID:1281995</ref> <ref>PMID:1374385</ref> <ref>PMID:1656963</ref> <ref>PMID:1657923</ref> [https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Escherichia virus T4]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Lysozyme]]
+[[Category: Cao C]]
-[[Category: Cao, C]]
+[[Category: Wu B]]
-[[Category: Wu, B]]
+[[Category: Zhang XC]]
-[[Category: Zhang, X C]]
+[[Category: Zhao Q]]
-[[Category: Zhao, Q]]
-[[Category: Complex]]
-[[Category: G protein-coupled receptor]]
-[[Category: Platelet-activating factor receptor]]
-[[Category: Signaling protein]]

5zkq

From Proteopedia

Revision as of 08:59, 22 November 2023

Crystal structure of the human platelet-activating factor receptor in complex with ABT-491

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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