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| | <StructureSection load='4pr6' size='340' side='right'caption='[[4pr6]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='4pr6' size='340' side='right'caption='[[4pr6]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4pr6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cx0 1cx0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PR6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PR6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4pr6]] 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=1cx0 1cx0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PR6 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4pr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pr6 OCA], [https://pdbe.org/4pr6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4pr6 RCSB], [https://www.ebi.ac.uk/pdbsum/4pr6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4pr6 ProSAT]</span></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4prf|4prf]]</td></tr>
| + | |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNRPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4pr6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pr6 OCA], [http://pdbe.org/4pr6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pr6 RCSB], [http://www.ebi.ac.uk/pdbsum/4pr6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pr6 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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Ribozyme|Ribozyme]] | + | *[[Ribozyme 3D structures|Ribozyme 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Doudna, J A]] | + | [[Category: Doudna JA]] |
| - | [[Category: Jain, S]] | + | [[Category: Jain S]] |
| - | [[Category: Kapral, G J]] | + | [[Category: Kapral GJ]] |
| - | [[Category: Noeske, J]] | + | [[Category: Noeske J]] |
| - | [[Category: Richardson, D C]] | + | [[Category: Richardson DC]] |
| - | [[Category: Richardson, J S]] | + | [[Category: Richardson JS]] |
| - | [[Category: Base sequence]]
| + | |
| - | [[Category: Binding site]]
| + | |
| - | [[Category: Catalysis]]
| + | |
| - | [[Category: Catalytic]]
| + | |
| - | [[Category: Cloning]]
| + | |
| - | [[Category: Computer graphic]]
| + | |
| - | [[Category: Escherichia coli]]
| + | |
| - | [[Category: Hepatitis delta virus]]
| + | |
| - | [[Category: Model]]
| + | |
| - | [[Category: Molecular]]
| + | |
| - | [[Category: Molecular sequence data]]
| + | |
| - | [[Category: Nucleic acid conformation]]
| + | |
| - | [[Category: Ribonucleoprotein]]
| + | |
| - | [[Category: Rna]]
| + | |
| - | [[Category: Rna binding protein-rna complex]]
| + | |
| - | [[Category: Rna binding protein/rna]]
| + | |
| - | [[Category: Rna-binding protein]]
| + | |
| - | [[Category: U1 small nuclear]]
| + | |
| - | [[Category: Viral]]
| + | |
| Structural highlights
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]
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[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ 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
- ↑ Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS. New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. Nucleic Acids Res. 2014 Oct 17. pii: gku992. PMID:25326328 doi:http://dx.doi.org/10.1093/nar/gku992
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