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1tp7

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Revision as of 11:57, 24 December 2020

Crystal Structure of the RNA-dependent RNA Polymerase from Human Rhinovirus 16

Structural highlights

1tp7 is a 4 chain structure with sequence from Hrv-16. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Gene:	3D (HRV-16)
Activity:	RNA-directed RNA polymerase, with EC number 2.7.7.48
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[POLG_HRV16] 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. 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 (By similarity). 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

Picornaviruses utilize virally encoded RNA polymerase and a uridylylated protein primer to ensure replication of the entire viral genome. The molecular details of this mechanism are not well understood due to the lack of structural information. We report the crystal structure of human rhinovirus 16 3D RNA-dependent RNA polymerase (HRV16 3Dpol) at a 2.4-A resolution, representing the first complete polymerase structure from the Picornaviridae family. HRV16 3Dpol shares the canonical features of other known polymerase structures and contains an N-terminal region that tethers the fingers and thumb subdomains, forming a completely encircled active site cavity which is accessible through a small tunnel on the backside of the molecule. The small thumb subdomain contributes to the formation of a large cleft on the front face of the polymerase which also leads to the active site. The cleft appears large enough to accommodate a template:primer duplex during RNA elongation or a protein primer during the uridylylation stage of replication initiation. Based on the structural features of HRV16 3Dpo1 and the catalytic mechanism known for all polymerases, a front-loading model for uridylylation is proposed.

Crystal structure of complete rhinovirus RNA polymerase suggests front loading of protein primer.,Appleby TC, Luecke H, Shim JH, Wu JZ, Cheney IW, Zhong W, Vogeley L, Hong Z, Yao N J Virol. 2005 Jan;79(1):277-88. PMID:15596823^[1]

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

References

↑ Appleby TC, Luecke H, Shim JH, Wu JZ, Cheney IW, Zhong W, Vogeley L, Hong Z, Yao N. Crystal structure of complete rhinovirus RNA polymerase suggests front loading of protein primer. J Virol. 2005 Jan;79(1):277-88. PMID:15596823 doi:79/1/277

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1tp7"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the RNA-dependent RNA Polymerase from Human Rhinovirus 16==
-<StructureSection load='1tp7' size='340' side='right' caption='[[1tp7]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='1tp7' size='340' side='right'caption='[[1tp7]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1tp7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-16 Hrv-16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TP7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TP7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1tp7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Hrv-16 Hrv-16]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TP7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1TP7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMX:3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE'>DMX</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMX:3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE'>DMX</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">3D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31708 HRV-16])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </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=1tp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tp7 OCA], [http://pdbe.org/1tp7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tp7 RCSB], [http://www.ebi.ac.uk/pdbsum/1tp7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tp7 ProSAT]</span></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=1tp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tp7 OCA], [http://pdbe.org/1tp7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tp7 RCSB], [http://www.ebi.ac.uk/pdbsum/1tp7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tp7 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 36: / Line 36: @@
 </StructureSection>
 [[Category: Hrv-16]]
+[[Category: Large Structures]]
 [[Category: RNA-directed RNA polymerase]]
 [[Category: Appleby, T C]]

1tp7

From Proteopedia

Revision as of 11:57, 24 December 2020

Crystal Structure of the RNA-dependent RNA Polymerase from Human Rhinovirus 16

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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