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.

2w42

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:55, 25 June 2020

THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH A 16NT DNA DUPLEX.

Structural highlights

2w42 is a 6 chain structure with sequence from Arcfl. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	2bgg, 1w9h
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PIWI_ARCFU] Required for RNA-mediated gene silencing (RNAi). Binds to short RNAs such as short interfering RNAs (siRNAs), and may cleave or repress the translation of mRNAs which are complementary to them (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

Target recognition in RNA silencing is governed by the "seed sequence" of a guide RNA strand associated with the PIWI/MID domain of an Argonaute protein in RISC. Using a reconstituted in vitro target recognition system, we show that a model PIWI/MID domain protein confers position-dependent tightening and loosening of guide-strand-target interactions. Over the seed sequence, the interaction affinity is enhanced up to approximately 300-fold. Enhancement is achieved through a reduced entropy penalty for the interaction. In contrast, interactions 3' of the seed are inhibited. We quantified mismatched target recognition inside and outside the seed, revealing amplified discrimination at the third position in the seed mediated by the PIWI/MID domain. Thus, association of the guide strand with the PIWI/MID domain generates an enhanced affinity anchor site over the seed that can promote fidelity in target recognition and stabilize and guide the assembly of the active silencing complex.

Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein.,Parker JS, Parizotto EA, Wang M, Roe SM, Barford D Mol Cell. 2009 Jan 30;33(2):204-14. PMID:19187762^[1]

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

References

↑ Parker JS, Parizotto EA, Wang M, Roe SM, Barford D. Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Mol Cell. 2009 Jan 30;33(2):204-14. PMID:19187762 doi:S1097-2765(08)00853-8

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/2w42"

@@ Line 1: / Line 1: @@
 ==THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH A 16NT DNA DUPLEX.==
-<StructureSection load='2w42' size='340' side='right' caption='[[2w42]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='2w42' size='340' side='right'caption='[[2w42]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2w42]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2W42 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2w42]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W42 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2W42 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2bgg|2bgg]], [[1w9h|1w9h]]</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=2w42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w42 OCA], [http://pdbe.org/2w42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w42 RCSB], [http://www.ebi.ac.uk/pdbsum/2w42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2w42 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=2w42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w42 OCA], [http://pdbe.org/2w42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2w42 RCSB], [http://www.ebi.ac.uk/pdbsum/2w42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2w42 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Arcfl]]
+[[Category: Large Structures]]
 [[Category: Barford, D]]
 [[Category: Parker, J S]]

2w42

From Proteopedia

Revision as of 08:55, 25 June 2020

THE STRUCTURE OF A PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH A 16NT DNA DUPLEX.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox