3kpe

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{{Seed}}
 
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[[Image:3kpe.png|left|200px]]
 
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==Solution structure of the respiratory syncytial virus (RSV)six-helix bundle complexed with TMC353121, a small-moleucule inhibitor of RSV==
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The line below this paragraph, containing "STRUCTURE_3kpe", creates the "Structure Box" on the page.
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<StructureSection load='3kpe' size='340' side='right'caption='[[3kpe]], [[Resolution|resolution]] 1.47&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3kpe]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_respiratory_syncytial_virus_A2 Human respiratory syncytial virus A2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KPE FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.47&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=TM3:2-[[6-[[[2-(3-HYDROXYPROPYL)-5-METHYLPHENYL]AMINO]METHYL]-2-[[3-(4-MORPHOLINYL)PROPYL]AMINO]-1H-BENZIMIDAZOL-1-YL]METHYL]-6-METHYL-3-PYRIDINOL'>TM3</scene></td></tr>
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{{STRUCTURE_3kpe| PDB=3kpe | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kpe OCA], [https://pdbe.org/3kpe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kpe RCSB], [https://www.ebi.ac.uk/pdbsum/3kpe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kpe ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/FUS_HRSVA FUS_HRSVA] Class I viral fusion protein. Under the current model, the protein has at least 3 conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and plasma cell membrane fusion, the heptad repeat (HR) regions assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and plasma cell membranes. Directs fusion of viral and cellular membranes leading to delivery of the nucleocapsid into the cytoplasm. This fusion is pH independent and occurs directly at the outer cell membrane. The trimer of F1-F2 (protein F) interacts with glycoprotein G at the virion surface. Upon binding of G to heparan sulfate, the hydrophobic fusion peptide is unmasked and interacts with the cellular membrane, inducing the fusion between host cell and virion membranes. Notably, RSV fusion protein is able to interact directly with heparan sulfate and therefore actively participates in virus attachment. Furthermore, the F2 subunit was identifed as the major determinant of RSV host cell specificity. Later in infection, proteins F expressed at the plasma membrane of infected cells mediate fusion with adjacent cells to form syncytia, a cytopathic effect that could lead to tissue necrosis. The fusion protein is also able to trigger p53-dependent apoptosis.<ref>PMID:12663767</ref> <ref>PMID:18216092</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kp/3kpe_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kpe ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Six-helix bundle (6HB) formation is an essential step for many viruses that rely on a class I fusion protein to enter a target cell and initiate replication. Because the binding modes of small molecule inhibitors of 6HB formation are largely unknown, precisely how they disrupt 6HB formation remains unclear, and structure-based design of improved inhibitors is thus seriously hampered. Here we present the high resolution crystal structure of TMC353121, a potent inhibitor of respiratory syncytial virus (RSV), bound at a hydrophobic pocket of the 6HB formed by amino acid residues from both HR1 and HR2 heptad-repeats. Binding of TMC353121 stabilizes the interaction of HR1 and HR2 in an alternate conformation of the 6HB, in which direct binding interactions are formed between TMC353121 and both HR1 and HR2. Rather than completely preventing 6HB formation, our data indicate that TMC353121 inhibits fusion by causing a local disturbance of the natural 6HB conformation.
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===Solution structure of the respiratory syncytial virus (RSV)six-helix bundle complexed with TMC353121, a small-moleucule inhibitor of RSV===
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Binding of a potent small-molecule inhibitor of six-helix bundle formation requires interactions with both heptad-repeats of the RSV fusion protein.,Roymans D, De Bondt HL, Arnoult E, Geluykens P, Gevers T, Van Ginderen M, Verheyen N, Kim H, Willebrords R, Bonfanti JF, Bruinzeel W, Cummings MD, van Vlijmen H, Andries K Proc Natl Acad Sci U S A. 2009 Dec 4. PMID:19966279<ref>PMID:19966279</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19966279}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3kpe" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19966279 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19966279}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Human respiratory syncytial virus A2]]
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3KPE is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Human_respiratory_syncytial_virus_a2 Human respiratory syncytial virus a2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KPE OCA].
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[[Category: Large Structures]]
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[[Category: Andries K]]
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==Reference==
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[[Category: Arnoult E]]
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<ref group="xtra">PMID:19966279</ref><references group="xtra"/>
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[[Category: Cummings MD]]
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[[Category: Human respiratory syncytial virus a2]]
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[[Category: De Bondt H]]
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[[Category: Andries, K.]]
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[[Category: Roymans D]]
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[[Category: Arnoult, E.]]
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[[Category: Van Vlijmen H]]
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[[Category: Bondt, H De.]]
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[[Category: Cummings, M D.]]
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[[Category: Roymans, D.]]
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[[Category: Vlijmen, H Van.]]
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[[Category: Alpha helix]]
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[[Category: Coiled-coil]]
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[[Category: Envelope protein]]
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[[Category: Fusion protein]]
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[[Category: Glycoprotein]]
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[[Category: Host cell membrane]]
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[[Category: Host membrane]]
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[[Category: Lipoprotein]]
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[[Category: Membrane]]
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[[Category: Palmitate]]
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[[Category: Peptide/small-molecule complex]]
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[[Category: Transmembrane]]
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[[Category: Virion]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 3 08:53:55 2010''
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Current revision

Solution structure of the respiratory syncytial virus (RSV)six-helix bundle complexed with TMC353121, a small-moleucule inhibitor of RSV

PDB ID 3kpe

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OCA

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