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1zdi

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RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX

Structural highlights

1zdi is a 5 chain structure with sequence from Escherichia phage MS2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSD_BPMS2 Self-assembles to form the T=3 icosahedral virus shell that protects the viral nucleic acid. Acts as a translational repressor by binding with high specificity to a single stem-loop structure in the genomic RNA that contains the initiation codon of the gene for the viral replicase. Involved in virus assembly through the interaction between a capsid protein dimer and the multiple packaging signals present in the RNA genome.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

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

Crystal structures of two complexes between recombinant MS2 capsids and RNA operator fragments have been determined at 2.7 A resolution. The coat protein of the RNA bacteriophage MS2 is bifunctional; it forms the icosahedral virus shell to protect the viral nucleic acid and it acts as a translational repressor by binding with high specificity to a unique site on the RNA, a single stem-loop structure, containing the initiation codon of the gene for the viral replicase. In order to determine the structure of these protein-RNA complexes, we have used chemically synthesized variants of the stem-loop fragment and soaked them into crystals of recombinant capsids. The RNA stem-loop, as bound to the protein, forms a crescent-like structure and interacts with the surface of the beta-sheet of a coat protein dimer. It makes protein contacts with seven phosphate groups on the 5' side of the stem-loop, with a pyrimidine base at position -5, which stacks onto a tyrosine, and with two exposed adenine bases, one in the loop and one at a bulge in the stem. Replacement of the wild-type uridine with a cytosine at position -5 increases the affinity of the RNA to the dimer significantly. The complex with RNA stem-loop having cytosine at this position differs from that of the wild-type complex mainly by having one extra intramolecular RNA interaction and one extra water-mediated hydrogen bond.

The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions.,Valegard K, Murray JB, Stonehouse NJ, van den Worm S, Stockley PG, Liljas L J Mol Biol. 1997 Aug 1;270(5):724-38. PMID:9245600^[7]

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

References

↑ Horn WT, Tars K, Grahn E, Helgstrand C, Baron AJ, Lago H, Adams CJ, Peabody DS, Phillips SE, Stonehouse NJ, Liljas L, Stockley PG. Structural basis of RNA binding discrimination between bacteriophages Qbeta and MS2. Structure. 2006 Mar;14(3):487-95. PMID:16531233 doi:http://dx.doi.org/10.1016/j.str.2005.12.006
↑ Plevka P, Tars K, Liljas L. Crystal packing of a bacteriophage MS2 coat protein mutant corresponds to octahedral particles. Protein Sci. 2008 Oct;17(10):1731-9. Epub 2008 Jul 28. PMID:18662904 doi:10.1110/ps.036905.108
↑ Rolfsson O, Middleton S, Manfield IW, White SJ, Fan B, Vaughan R, Ranson NA, Dykeman E, Twarock R, Ford J, Kao CC, Stockley PG. Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2. J Mol Biol. 2016 Jan 29;428(2 Pt B):431-48. doi: 10.1016/j.jmb.2015.11.014. Epub , 2015 Dec 1. PMID:26608810 doi:http://dx.doi.org/10.1016/j.jmb.2015.11.014
↑ Golmohammadi R, Valegard K, Fridborg K, Liljas L. The refined structure of bacteriophage MS2 at 2.8 A resolution. J Mol Biol. 1993 Dec 5;234(3):620-39. PMID:8254664 doi:http://dx.doi.org/10.1006/jmbi.1993.1616
↑ Valegard K, Murray JB, Stonehouse NJ, van den Worm S, Stockley PG, Liljas L. The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions. J Mol Biol. 1997 Aug 1;270(5):724-38. PMID:9245600 doi:http://dx.doi.org/10.1006/jmbi.1997.1144
↑ van den Worm SH, Stonehouse NJ, Valegard K, Murray JB, Walton C, Fridborg K, Stockley PG, Liljas L. Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments. Nucleic Acids Res. 1998 Mar 1;26(5):1345-51. PMID:9469847
↑ Valegard K, Murray JB, Stonehouse NJ, van den Worm S, Stockley PG, Liljas L. The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions. J Mol Biol. 1997 Aug 1;270(5):724-38. PMID:9245600 doi:http://dx.doi.org/10.1006/jmbi.1997.1144

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/1zdi"

Categories: Escherichia phage MS2 | Large Structures | Liljas L | Valegard K | Van Den Worm S

@@ Line 1: / Line 1: @@
-[[Image:1zdi.png|left|200px]]
-<!--
+==RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX==
-The line below this paragraph, containing "STRUCTURE_1zdi", creates the "Structure Box" on the page.
+<StructureSection load='1zdi' size='340' side='right'caption='[[1zdi]], [[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'>[[1zdi]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_MS2 Escherichia phage MS2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZDI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZDI FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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=1zdi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zdi OCA], [https://pdbe.org/1zdi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zdi RCSB], [https://www.ebi.ac.uk/pdbsum/1zdi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zdi ProSAT]</span></td></tr>
--->
+</table>
-{{STRUCTURE_1zdi|  PDB=1zdi  |  SCENE=  }}
+== Function ==
+[https://www.uniprot.org/uniprot/CAPSD_BPMS2 CAPSD_BPMS2] Self-assembles to form the T=3 icosahedral virus shell that protects the viral nucleic acid. Acts as a translational repressor by binding with high specificity to a single stem-loop structure in the genomic RNA that contains the initiation codon of the gene for the viral replicase. Involved in virus assembly through the interaction between a capsid protein dimer and the multiple packaging signals present in the RNA genome.<ref>PMID:16531233</ref> <ref>PMID:18662904</ref> <ref>PMID:26608810</ref> <ref>PMID:8254664</ref> <ref>PMID:9245600</ref> <ref>PMID:9469847</ref>
+== 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/zd/1zdi_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=1zdi ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Crystal structures of two complexes between recombinant MS2 capsids and RNA operator fragments have been determined at 2.7 A resolution. The coat protein of the RNA bacteriophage MS2 is bifunctional; it forms the icosahedral virus shell to protect the viral nucleic acid and it acts as a translational repressor by binding with high specificity to a unique site on the RNA, a single stem-loop structure, containing the initiation codon of the gene for the viral replicase. In order to determine the structure of these protein-RNA complexes, we have used chemically synthesized variants of the stem-loop fragment and soaked them into crystals of recombinant capsids. The RNA stem-loop, as bound to the protein, forms a crescent-like structure and interacts with the surface of the beta-sheet of a coat protein dimer. It makes protein contacts with seven phosphate groups on the 5' side of the stem-loop, with a pyrimidine base at position -5, which stacks onto a tyrosine, and with two exposed adenine bases, one in the loop and one at a bulge in the stem. Replacement of the wild-type uridine with a cytosine at position -5 increases the affinity of the RNA to the dimer significantly. The complex with RNA stem-loop having cytosine at this position differs from that of the wild-type complex mainly by having one extra intramolecular RNA interaction and one extra water-mediated hydrogen bond.
-===RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX===
+The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions.,Valegard K, Murray JB, Stonehouse NJ, van den Worm S, Stockley PG, Liljas L J Mol Biol. 1997 Aug 1;270(5):724-38. PMID:9245600<ref>PMID:9245600</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_9245600}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1zdi" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 9245600 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9245600}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia phage MS2]]
-[[1zdi]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacterio_phage_ms2 Enterobacterio phage ms2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZDI OCA].
+[[Category: Large Structures]]
+[[Category: Liljas L]]
-==Reference==
+[[Category: Valegard K]]
-<ref group="xtra">PMID:009245600</ref><ref group="xtra">PMID:009461079</ref><ref group="xtra">PMID:015048824</ref><references group="xtra"/>
+[[Category: Van Den Worm S]]
-[[Category: Enterobacterio phage ms2]]
-[[Category: Liljas, L.]]
-[[Category: Valegard, K.]]
-[[Category: Worm, S Van Den.]]
-[[Category: Coat protein]]
-[[Category: Icosahedral virus]]
-[[Category: Rna fragment]]
-[[Category: Rna-binding]]
-[[Category: Viral protein capsid]]
-[[Category: Virus-rna complex]]

1zdi

From Proteopedia

Current revision

RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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