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6msf

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F6 APTAMER MS2 COAT PROTEIN COMPLEX

Structural highlights

6msf 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.
Method:	X-ray diffraction, Resolution 2.8Å
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

The crystal structure, at 2.8 A resolution, of an RNA aptamer bound to bacteriophage MS2 coat protein has been determined. It provides an opportunity to compare the interactions of MS2 coat protein and wild type operator with those of an aptamer, whose secondary structure differs from the wild type RNA in having a three-base loop (compared to a tetraloop) and an additional base pair between this loop and the sequence-specific recognition element in the stem. The RNA binds in the same location on the coat protein as the wild type operator and maintains many of the same RNA-protein interactions. In order to achieve this, the RNA stem loop undergoes a concerted rearrangement of the 3' side while leaving the 5' side and the loop interactions largely unchanged, illustrating the ability of RNA to present similar molecular recognition surfaces from distinct primary and secondary structures.

Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution.,Convery MA, Rowsell S, Stonehouse NJ, Ellington AD, Hirao I, Murray JB, Peabody DS, Phillips SE, Stockley PG Nat Struct Biol. 1998 Feb;5(2):133-9. PMID:9461079^[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
↑ Convery MA, Rowsell S, Stonehouse NJ, Ellington AD, Hirao I, Murray JB, Peabody DS, Phillips SE, Stockley PG. Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution. Nat Struct Biol. 1998 Feb;5(2):133-9. PMID:9461079

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/6msf"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:6msf.png|left|200px]]
-<!--
+==F6 APTAMER MS2 COAT PROTEIN COMPLEX==
-The line below this paragraph, containing "STRUCTURE_6msf", creates the "Structure Box" on the page.
+<StructureSection load='6msf' size='340' side='right'caption='[[6msf]], [[Resolution|resolution]] 2.80&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'>[[6msf]] 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=6MSF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MSF 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]] 2.8&#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=6msf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6msf OCA], [https://pdbe.org/6msf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6msf RCSB], [https://www.ebi.ac.uk/pdbsum/6msf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6msf ProSAT]</span></td></tr>
-{{STRUCTURE_6msf|  PDB=6msf  |  SCENE=  }}
+</table>
+== 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/ms/6msf_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=6msf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure, at 2.8 A resolution, of an RNA aptamer bound to bacteriophage MS2 coat protein has been determined. It provides an opportunity to compare the interactions of MS2 coat protein and wild type operator with those of an aptamer, whose secondary structure differs from the wild type RNA in having a three-base loop (compared to a tetraloop) and an additional base pair between this loop and the sequence-specific recognition element in the stem. The RNA binds in the same location on the coat protein as the wild type operator and maintains many of the same RNA-protein interactions. In order to achieve this, the RNA stem loop undergoes a concerted rearrangement of the 3' side while leaving the 5' side and the loop interactions largely unchanged, illustrating the ability of RNA to present similar molecular recognition surfaces from distinct primary and secondary structures.
-===F6 APTAMER MS2 COAT PROTEIN COMPLEX===
+Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution.,Convery MA, Rowsell S, Stonehouse NJ, Ellington AD, Hirao I, Murray JB, Peabody DS, Phillips SE, Stockley PG Nat Struct Biol. 1998 Feb;5(2):133-9. PMID:9461079<ref>PMID:9461079</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_9461079}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 6msf" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 9461079 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_9461079}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia phage MS2]]
-MSF is a [[Single protein]] structure of 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=6MSF OCA].
+[[Category: Large Structures]]
+[[Category: Convery MA]]
-==Reference==
+[[Category: Ellington AD]]
-Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution., Convery MA, Rowsell S, Stonehouse NJ, Ellington AD, Hirao I, Murray JB, Peabody DS, Phillips SE, Stockley PG, Nat Struct Biol. 1998 Feb;5(2):133-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9461079 9461079]
+[[Category: Hirao I]]
-[[Category: Enterobacterio phage ms2]]
+[[Category: Murray JB]]
-[[Category: Single protein]]
+[[Category: Peabody DS]]
-[[Category: Convery, M A.]]
+[[Category: Phillips SEV]]
-[[Category: Ellington, A D.]]
+[[Category: Rowsell S]]
-[[Category: Hirao, I.]]
+[[Category: Stockley PG]]
-[[Category: Murray, J B.]]
+[[Category: Stonehouse NJ]]
-[[Category: Peabody, D S.]]
-[[Category: Phillips, S E.V.]]
-[[Category: Rowsell, S.]]
-[[Category: Stockley, P G.]]
-[[Category: Stonehouse, N J.]]
-[[Category: Bacteriophage ms2]]
-[[Category: Icosahedral virus]]
-[[Category: Rna aptamer]]
-[[Category: Rna stem loop]]
-[[Category: Viral coat protein/rna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul  3 14:22:16 2008''

6msf

From Proteopedia

Current revision

F6 APTAMER MS2 COAT PROTEIN COMPLEX

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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