4rhv

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:49, 22 May 2024) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:4rhv.png|left|200px]]
 
-
<!--
+
==THE USE OF MOLECULAR-REPLACEMENT PHASES FOR THE REFINEMENT OF THE HUMAN RHINOVIRUS 14 STRUCTURE==
-
The line below this paragraph, containing "STRUCTURE_4rhv", creates the "Structure Box" on the page.
+
<StructureSection load='4rhv' size='340' side='right'caption='[[4rhv]], [[Resolution|resolution]] 3.00&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'>[[4rhv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhinovirus_B14 Rhinovirus B14]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2rhv 2rhv] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rhv 1rhv]. The August 2001 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Poliovirus and Rhinovirus'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2001_8 10.2210/rcsb_pdb/mom_2001_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RHV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RHV 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]] 3&#8491;</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=4rhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rhv OCA], [https://pdbe.org/4rhv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rhv RCSB], [https://www.ebi.ac.uk/pdbsum/4rhv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rhv ProSAT]</span></td></tr>
-
{{STRUCTURE_4rhv| PDB=4rhv | SCENE= }}
+
</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/rh/4rhv_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=4rhv ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The structure of human rhinovirus 14 has been refined, by the method of restrained least squares, to an R factor of 0.16 for various random samples between 6 and 3 A resolution with F greater than 3 sigma (F). As a first step the non-crystallographic symmetry parameters were optimized using the initial atomic model in a rigid-body refinement procedure. Phase determination by the molecular-replacement phase extension and refinement procedure was continued to 2.94 A resolution, employing the improved non-crystallographic symmetry operators. The resultant structure-factor phases and weights, together with the measured amplitudes, constituted the X-ray observations used in the restrained refinement. The Hendrickson-Konnert program system [Konnert &amp; Hendrickson (1980). Acta Cryst. A36, 344-350] was modified to incorporate non-crystallographic symmetry constrains and structure-factor phases as observations. The non-bonded contacts between subunits related by non-crystallographic symmetry were also restrained.
-
===THE USE OF MOLECULAR-REPLACEMENT PHASES FOR THE REFINEMENT OF THE HUMAN RHINOVIRUS 14 STRUCTURE===
+
The use of molecular-replacement phases for the refinement of the human rhinovirus 14 structure.,Arnold E, Rossmann MG Acta Crystallogr A. 1988 May 1;44 ( Pt 3):270-82. PMID:2856083<ref>PMID:2856083</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 4rhv" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_2856083}}, adds the Publication Abstract to the page
+
*[[Human rhinovirus|Human rhinovirus]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 2856083 is the PubMed ID number.
+
*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
-
-->
+
== References ==
-
{{ABSTRACT_PUBMED_2856083}}
+
<references/>
-
 
+
__TOC__
-
==About this Structure==
+
</StructureSection>
-
4RHV is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Human_rhinovirus_14 Human rhinovirus 14]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rhv 1rhv]. The August 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Poliovirus and Rhinovirus'' by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_8 10.2210/rcsb_pdb/mom_2001_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RHV OCA].
+
[[Category: Large Structures]]
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:2856083</ref><references group="xtra"/>
+
-
[[Category: Human rhinovirus 14]]
+
[[Category: Poliovirus and Rhinovirus]]
[[Category: Poliovirus and Rhinovirus]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: RCSB PDB Molecule of the Month]]
-
[[Category: Arnold, E.]]
+
[[Category: Rhinovirus B14]]
-
[[Category: Rossmann, M G.]]
+
[[Category: Arnold E]]
-
[[Category: Icosahedral virus]]
+
[[Category: Rossmann MG]]
-
[[Category: Rhinovirus coat protein]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 21 09:11:44 2010''
+

Current revision

THE USE OF MOLECULAR-REPLACEMENT PHASES FOR THE REFINEMENT OF THE HUMAN RHINOVIRUS 14 STRUCTURE

PDB ID 4rhv

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4rhv"
Personal tools