1k5m: Difference between revisions

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-{{Seed}}
-[[Image:1k5m.png|left|200px]]
-<!--
+==Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2==
-The line below this paragraph, containing "STRUCTURE_1k5m", creates the "Structure Box" on the page.
+<StructureSection load='1k5m' size='340' side='right'caption='[[1k5m]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1k5m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/HIV-1_M:B_MN HIV-1 M:B_MN] and [https://en.wikipedia.org/wiki/Rhinovirus_B14 Rhinovirus B14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K5M FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SPH:SPHINGOSINE'>SPH</scene></td></tr>
-{{STRUCTURE_1k5m|  PDB=1k5m  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5m OCA], [https://pdbe.org/1k5m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k5m RCSB], [https://www.ebi.ac.uk/pdbsum/1k5m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k5m ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/POLG_HRV14 POLG_HRV14] Capsid proteins VP1, VP2, VP3 and VP4 form a closed capsid enclosing the viral positive strand RNA genome. VP4 lies on the inner surface of the protein shell formed by VP1, VP2 and VP3. All the three latter proteins contain a beta-sheet structure called beta-barrel jelly roll. Together they form an icosahedral capsid (T=3) composed of 60 copies of each VP1, VP2, and VP3, with a diameter of approximately 300 Angstroms. VP1 is situated at the 12 fivefold axes, whereas VP2 and VP3 are located at the quasi-sixfold axes (By similarity). The capsid interacts with human ICAM1 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin- and caveolin-independent endocytosis.  VP0 precursor is a component of immature procapsids (By similarity).  Protein 2A is a cysteine protease that is responsible for the cleavage between the P1 and P2 regions. It cleaves the host translation initiation factor EIF4G1, in order to shut down the capped cellular mRNA transcription (By similarity).  Protein 2B affects membrane integrity and cause an increase in membrane permeability (By similarity).  Protein 2C associates with and induces structural rearrangements of intracellular membranes. It displays RNA-binding, nucleotide binding and NTPase activities (By similarity).  Protein 3A, via its hydrophobic domain, serves as membrane anchor (By similarity).  Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity).  RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k5/1k5m_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1k5m ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report the 2.7 A resolution structure of a chimeric rhinovirus, MN-III-2, that displays part of the HIV-1 gp120 V3 loop and elicits HIV-neutralizing antibodies. The V3 loop insert is dominated by two type I beta turns. The structures of two adjacent tripeptides resemble those of analogous segments in three Fab/V3 loop peptide complexes. Although two of the three corresponding antibodies bind and neutralize MN-III-2 well, only one of the three can bind without significant rearrangement. These results suggest that the V3 loop insert: (1) can share some local conformational similarity to V3 loop sequences presented on different structural frameworks; (2) must be able to adopt multiple conformations, even in a relatively constrained environment; and (3) may mimic the conformational variability of the epitope on HIV-1, increasing the likelihood of eliciting appropriate neutralizing immune responses.
-===Crystal Structure of a Human Rhinovirus Type 14:Human Immunodeficiency Virus Type 1 V3 Loop Chimeric Virus MN-III-2===
+Crystal structure of a human rhinovirus that displays part of the HIV-1 V3 loop and induces neutralizing antibodies against HIV-1.,Ding J, Smith AD, Geisler SC, Ma X, Arnold GF, Arnold E Structure. 2002 Jul;10(7):999-1011. PMID:12121655<ref>PMID:12121655</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1k5m" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12121655}}, adds the Publication Abstract to the page
+*[[Human rhinovirus|Human rhinovirus]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12121655 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12121655}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: HIV-1 M:B_MN]]
-K5M is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Human_rhinovirus_14 Human rhinovirus 14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5M OCA].
+[[Category: Large Structures]]
+[[Category: Rhinovirus B14]]
-==Reference==
+[[Category: Arnold E]]
-<ref group="xtra">PMID:12121655</ref><references group="xtra"/>
+[[Category: Arnold GF]]
-[[Category: Human rhinovirus 14]]
+[[Category: Ding J]]
-[[Category: Arnold, E.]]
+[[Category: Geisler SC]]
-[[Category: Arnold, G F.]]
+[[Category: Ma X]]
-[[Category: Ding, J.]]
+[[Category: Smith AD]]
-[[Category: Geisler, S C.]]
-[[Category: Ma, X.]]
-[[Category: Smith, A D.]]
-[[Category: Beta turn]]
-[[Category: Engineered rhinovirus]]
-[[Category: Hiv-1 v3 loop]]
-[[Category: Icosahedral virus]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 07:59:09 2009''