2oj3

From Proteopedia

(Difference between revisions)

Revision as of 12:57, 9 June 2021

Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and cobalt hexammine (Co(NH3)63+)

Structural highlights

2oj3 is a 2 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	SNRPA (HUMAN)
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]

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 hepatitis delta virus (HDV) ribozyme catalyzes viral RNA self-cleavage through general acid-base chemistry in which an active-site cytidine and at least one metal ion are involved. Monovalent metal ions support slow catalysis and were proposed to substitute for structural, but not catalytic, divalent metal ions in the RNA. To investigate the role of monovalent cations in ribozyme structure and function, we determined the crystal structure of the precursor HDV ribozyme in the presence of thallium ions (Tl(+)). Two Tl(+) ions can occupy a previously observed divalent metal ion hexahydrate-binding site located near the scissile phosphate, but are easily competed away by cobalt hexammine, a magnesium hexahydrate mimic and potent reaction inhibitor. Intriguingly, a third Tl(+) ion forms direct inner-sphere contacts with the ribose 2'-OH nucleophile and the pro-S(p) scissile phosphate oxygen. We discuss possible structural and catalytic implications of monovalent cation binding for the HDV ribozyme mechanism.

Structural roles of monovalent cations in the HDV ribozyme.,Ke A, Ding F, Batchelor JD, Doudna JA Structure. 2007 Mar;15(3):281-7. PMID:17355864^[2]

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

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
↑ Ke A, Ding F, Batchelor JD, Doudna JA. Structural roles of monovalent cations in the HDV ribozyme. Structure. 2007 Mar;15(3):281-7. PMID:17355864 doi:http://dx.doi.org/10.1016/j.str.2007.01.017

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2oj3"

@@ Line 1: / Line 1: @@
 ==Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and cobalt hexammine (Co(NH3)63+)==
-<StructureSection load='2oj3' size='340' side='right' caption='[[2oj3]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='2oj3' size='340' side='right'caption='[[2oj3]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2oj3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OJ3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OJ3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2oj3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OJ3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNRPA ([https://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=2oj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oj3 OCA], [http://pdbe.org/2oj3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oj3 RCSB], [http://www.ebi.ac.uk/pdbsum/2oj3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2oj3 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=2oj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oj3 OCA], [https://pdbe.org/2oj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oj3 RCSB], [https://www.ebi.ac.uk/pdbsum/2oj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oj3 ProSAT]</span></td></tr>
 </table>
 == 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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Nucleoprotein|Nucleoprotein]]
+*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
 *[[Ribozyme|Ribozyme]]
 == References ==
@@ Line 38: / Line 38: @@
 </StructureSection>
 [[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Batchelor, J D]]
 [[Category: Ding, F]]

2oj3

From Proteopedia

Revision as of 12:57, 9 June 2021

Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and cobalt hexammine (Co(NH3)63+)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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