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.
1m5o
From Proteopedia
(Difference between revisions)
| Line 3: | Line 3: | ||
<StructureSection load='1m5o' size='340' side='right'caption='[[1m5o]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='1m5o' size='340' side='right'caption='[[1m5o]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[1m5o]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/ | + | <table><tr><td colspan='2'>[[1m5o]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M5O FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AVC:ADENOSINE-5-MONOPHOSPHATE-2,3-VANADATE'>AVC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=1m5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5o OCA], [https://pdbe.org/1m5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m5o RCSB], [https://www.ebi.ac.uk/pdbsum/1m5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5o ProSAT]</span></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=1m5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5o OCA], [https://pdbe.org/1m5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m5o RCSB], [https://www.ebi.ac.uk/pdbsum/1m5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5o ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
| - | + | [https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref> | |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
| Line 22: | Line 20: | ||
</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=1m5o 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=1m5o ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | The hairpin ribozyme catalyzes sequence-specific cleavage of RNA through transesterification of the scissile phosphate. Vanadate has previously been used as a transition state mimic of protein enzymes that catalyze the same reaction. Comparison of the 2.2 angstrom resolution structure of a vanadate-hairpin ribozyme complex with structures of precursor and product complexes reveals a rigid active site that makes more hydrogen bonds to the transition state than to the precursor or product. Because of the paucity of RNA functional groups capable of general acid-base or electrostatic catalysis, transition state stabilization is likely to be an important catalytic strategy for ribozymes. | ||
| - | |||
| - | Transition state stabilization by a catalytic RNA.,Rupert PB, Massey AP, Sigurdsson ST, Ferre-D'Amare AR Science. 2002 Nov 15;298(5597):1421-4. Epub 2002 Oct 10. PMID:12376595<ref>PMID:12376595</ref> | ||
| - | |||
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 1m5o" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]] | *[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]] | ||
| - | *[[Ribozyme|Ribozyme]] | + | *[[Ribozyme 3D structures|Ribozyme 3D structures]] |
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Homo sapiens]] |
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Ferre-D'Amare AR]] |
| - | [[Category: Massey | + | [[Category: Massey AP]] |
| - | [[Category: Rupert | + | [[Category: Rupert PB]] |
| - | [[Category: Sigurdsson | + | [[Category: Sigurdsson ST]] |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
Transition State Stabilization by a Catalytic RNA
| |||||||||||
