1m5k

From Proteopedia

(Difference between revisions)

Revision as of 08:33, 2 December 2020

Crystal structure of a hairpin ribozyme in the catalytically-active conformation

Structural highlights

1m5k is a 6 chain structure with sequence from Human. This structure supersedes the now removed PDB entry 1hp6. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:	, ,
Related:	1m5o, 1m5p, 1m5v
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 hairpin ribozyme catalyses sequence-specific cleavage of RNA. The active site of this natural RNA results from the docking of two irregular helices: stems A and B. One strand of stem A harbours the scissile bond. The 2.4 A resolution structure of a hairpin ribozyme-inhibitor complex reveals that the ribozyme aligns the 2'-OH nucleophile and the 5'-oxo leaving group by twisting apart the nucleotides that flank the scissile phosphate. The base of the nucleotide preceding the cleavage site is stacked within stem A; the next nucleotide, a conserved guanine, is extruded from stem A and accommodated by a highly complementary pocket in the minor groove of stem B. Metal ions are absent from the active site. The bases of four conserved purines are positioned potentially to serve as acid-base catalysts. This is the first structure determination of a fully assembled ribozyme active site that catalyses a phosphodiester cleavage without recourse to metal ions.

Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis.,Rupert PB, Ferre-D'Amare AR Nature. 2001 Apr 12;410(6830):780-6. PMID:11298439^[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
↑ Rupert PB, Ferre-D'Amare AR. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature. 2001 Apr 12;410(6830):780-6. PMID:11298439 doi:10.1038/35071009

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/1m5k"

@@ Line 1: / Line 1: @@
 ==Crystal structure of a hairpin ribozyme in the catalytically-active conformation==
-<StructureSection load='1m5k' size='340' side='right' caption='[[1m5k]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='1m5k' size='340' side='right'caption='[[1m5k]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1m5k]] is a 6 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=1hp6 1hp6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M5K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1m5k]] is a 6 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=1hp6 1hp6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M5K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1M5K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=IU:5-IODOURIDINE-5-MONOPHOSPHATE'>IU</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1m5o|1m5o]], [[1m5p|1m5p]], [[1m5v|1m5v]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1m5o|1m5o]], [[1m5p|1m5p]], [[1m5v|1m5v]]</div></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=1m5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5k OCA], [http://pdbe.org/1m5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m5k RCSB], [http://www.ebi.ac.uk/pdbsum/1m5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5k 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=1m5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5k OCA], [http://pdbe.org/1m5k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m5k RCSB], [http://www.ebi.ac.uk/pdbsum/1m5k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5k ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 34: / Line 34: @@
 ==See Also==
 *[[Hairpin Ribozyme|Hairpin Ribozyme]]
+*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
 *[[Ribozyme|Ribozyme]]
 == References ==
@@ Line 40: / Line 41: @@
 </StructureSection>
 [[Category: Human]]
+[[Category: Large Structures]]
 [[Category: Amare, A R.Ferre-D]]
 [[Category: Rupert, P B]]

1m5k

From Proteopedia

Revision as of 08:33, 2 December 2020

Crystal structure of a hairpin ribozyme in the catalytically-active conformation

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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