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==A Second Look at the HDV Ribozyme Structure and Dynamics.==
==A Second Look at the HDV Ribozyme Structure and Dynamics.==
<StructureSection load='4prf' size='340' side='right' caption='[[4prf]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
<StructureSection load='4prf' size='340' side='right'caption='[[4prf]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4prf]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vc7 1vc7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PRF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PRF FirstGlance]. <br>
<table><tr><td colspan='2'>[[4prf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vc7 1vc7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PRF FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.395&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4pr6|4pr6]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></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=4prf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4prf OCA], [http://pdbe.org/4prf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4prf RCSB], [http://www.ebi.ac.uk/pdbsum/4prf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4prf 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=4prf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4prf OCA], [https://pdbe.org/4prf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4prf RCSB], [https://www.ebi.ac.uk/pdbsum/4prf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4prf ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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> 
[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>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in 1998, followed by structures of uncleaved, mutant-inhibited and ion-complexed forms. Recently, methods have been developed that make the task of modeling RNA structure and dynamics significantly easier and more reliable. We have used ERRASER and PHENIX to rebuild and re-refine the cleaved and cis-acting C75U-inhibited structures of the HDV ribozyme. The results correct local conformations and identify alternates for RNA residues, many in functionally important regions, leading to improved R values and model validation statistics for both structures. We compare the rebuilt structures to a higher resolution, trans-acting deoxy-inhibited structure of the ribozyme, and conclude that although both inhibited structures are consistent with the currently accepted hammerhead-like mechanism of cleavage, they do not add direct structural evidence to the biochemical and modeling data. However, the rebuilt structures (PDBs: 4PR6, 4PRF) provide a more robust starting point for research on the dynamics and catalytic mechanism of the HDV ribozyme and demonstrate the power of new techniques to make significant improvements in RNA structures that impact biologically relevant conclusions.
 
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.,Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS Nucleic Acids Res. 2014 Oct 17. pii: gku992. PMID:25326328<ref>PMID:25326328</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4prf" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribozyme|Ribozyme]]
*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
*[[Ribozyme 3D structures|Ribozyme 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Doudna, J A]]
[[Category: Homo sapiens]]
[[Category: Jain, S]]
[[Category: Large Structures]]
[[Category: Kapral, G J]]
[[Category: Doudna JA]]
[[Category: Noeske, J]]
[[Category: Jain S]]
[[Category: Richardson, D C]]
[[Category: Kapral GJ]]
[[Category: Richardson, J S]]
[[Category: Noeske J]]
[[Category: Hdv]]
[[Category: Richardson DC]]
[[Category: Precursor]]
[[Category: Richardson JS]]
[[Category: Ribozyme]]
[[Category: Rna]]
[[Category: Rna binding protein-rna complex]]
[[Category: Translation-rna complex]]
[[Category: U1a]]

Latest revision as of 15:42, 1 March 2024

A Second Look at the HDV Ribozyme Structure and Dynamics.A Second Look at the HDV Ribozyme Structure and Dynamics.

Structural highlights

4prf is a 2 chain structure with sequence from Homo sapiens. This structure supersedes the now removed PDB entry 1vc7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.395Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1]

See Also

References

  1. ↑ Lutz CS, Cooke C, O'Connor JP, Kobayashi R, Alwine JC. The snRNP-free U1A (SF-A) complex(es): identification of the largest subunit as PSF, the polypyrimidine-tract binding protein-associated splicing factor. RNA. 1998 Dec;4(12):1493-9. PMID:9848648

4prf, resolution 2.40Å

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