This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2rm2

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 07:34, 5 August 2016

STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES

Structural highlights

2rm2 is a 4 chain structure with sequence from Hrv-14. This structure supersedes the now removed PDB entry 1rm2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1r08, 1r09, 2r04, 2r06, 2r07, 2rr1, 2rs1, 2rs3, 2rs5
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

X-Ray diffraction data have been obtained for nine related antiviral agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (approximately 60%) occupancies of these compounds in the crystal, (2) the large (up to 7.9 A) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps. The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the beta-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the beta-barrel.

Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses.,Badger J, Minor I, Oliveira MA, Smith TJ, Rossmann MG Proteins. 1989;6(1):1-19. PMID:2558377^[1]

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

References

↑ Badger J, Minor I, Oliveira MA, Smith TJ, Rossmann MG. Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses. Proteins. 1989;6(1):1-19. PMID:2558377 doi:http://dx.doi.org/10.1002/prot.340060102

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2rm2"

@@ Line 1: / Line 1: @@
 ==STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES==
 <StructureSection load='2rm2' size='340' side='right' caption='[[2rm2]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_rhinovirus_b14 Human rhinovirus b14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2rm2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-14 Hrv-14]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rm2 1rm2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RM2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RM2 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=W43:5-(7-(6-CHLORO-4-(5-HYDRO-4-METHYL-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL+ISOXAZOLE'>W43</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1r08|1r08]], [[1r09|1r09]], [[2r04|2r04]], [[2r06|2r06]], [[2r07|2r07]], [[2rr1|2rr1]], [[2rs1|2rs1]], [[2rs3|2rs3]], [[2rs5|2rs5]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rm2 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rm2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rm2 OCA], [http://pdbe.org/2rm2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rm2 RCSB], [http://www.ebi.ac.uk/pdbsum/2rm2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rm2 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2rm2 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2rm2" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Human rhinovirus b14]]
+[[Category: Hrv-14]]
 [[Category: Badger, J]]
 [[Category: Rossmann, M G]]

2rm2

From Proteopedia

Revision as of 07:34, 5 August 2016

STRUCTURAL ANALYSIS OF ANTIVIRAL AGENTS THAT INTERACT WITH THE CAPSID OF HUMAN RHINOVIRUSES

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox