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| | ==CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTION PRIMER TRNA(LYS3)== | | ==CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTION PRIMER TRNA(LYS3)== |
| - | <StructureSection load='1fir' size='340' side='right' caption='[[1fir]], [[Resolution|resolution]] 3.30Å' scene=''> | + | <StructureSection load='1fir' size='340' side='right'caption='[[1fir]], [[Resolution|resolution]] 3.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1fir]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1FIR FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1fir]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FIR 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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 3.3Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=12A:2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE-5-MONOPHOSPHATE'>12A</scene>, <scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=2MU:2,5-DIMETHYLURIDINE-5-MONOPHOSPHATE'>2MU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=70U:5-(O-METHYLACETO)-2-THIO-2-DEOXY-URIDINE-5-MONOPHOSPHATE'>70U</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=12A:2-METHYLTHIO-N6-(AMINOCARBONYL-L-THREONYL)-ADENOSINE-5-MONOPHOSPHATE'>12A</scene>, <scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=2MU:2,5-DIMETHYLURIDINE-5-MONOPHOSPHATE'>2MU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=70U:5-(O-METHYLACETO)-2-THIO-2-DEOXY-URIDINE-5-MONOPHOSPHATE'>70U</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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=1fir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fir OCA], [http://pdbe.org/1fir PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1fir RCSB], [http://www.ebi.ac.uk/pdbsum/1fir PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1fir 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=1fir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fir OCA], [https://pdbe.org/1fir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fir RCSB], [https://www.ebi.ac.uk/pdbsum/1fir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fir ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | ==See Also== | | ==See Also== |
| - | *[[TRNA|TRNA]] | + | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Bos taurus]] | | [[Category: Bos taurus]] |
| - | [[Category: Benas, P]] | + | [[Category: Large Structures]] |
| - | [[Category: Dumas, P]] | + | [[Category: Benas P]] |
| - | [[Category: Amino acid transport]] | + | [[Category: Dumas P]] |
| - | [[Category: Canonical anticodon]]
| + | |
| - | [[Category: Canonical trna structure]]
| + | |
| - | [[Category: Codon/anticodon mimicry]]
| + | |
| - | [[Category: Frameshifting]]
| + | |
| - | [[Category: Hiv-1 primer trna]]
| + | |
| - | [[Category: Mammalian transfert ribonucleic acid]]
| + | |
| - | [[Category: Modified base]]
| + | |
| - | [[Category: Rna]]
| + | |
| Structural highlights
1fir is a 1 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 3.3Å |
| Ligands: | , , , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
We have solved to 3.3 A resolution the crystal structure of the HIV reverse-transcription primer tRNA(Lys,3). The overall structure is exactly comparable to the well-known L-shape structure first revealed by yeast tRNA(Phe). In particular, it unambiguously shows a canonical anticodon loop. This contradicts previous results in short RNA fragment studies and leads us to conclude that neither frameshifting specificities of tRNA(Lys) nor tRNA(Lys,3) primer selection by HIV are due to a specific three-dimensional anticodon structure. Comparison of our structure with the results of an NMR study on a hairpin representing a nonmodified anticodon stem-loop makes plausible the conclusion that chemical modifications of the wobble base U34 to 5-methoxycarbonyl-methyl-2-thiouridine and of A37 to 2-methylthio-N-6-threonylcarbamoyl-adenosine would be responsible for a canonical 7-nt anticodon-loop structure, whereas the unmodified form would result in a noncanonical UUU short triloop. The hexagonal crystal packing is remarkable and shows tight dimers of tRNAs forming a right-handed double superhelix. Within the dimers, the tRNAs are associated head-to-tail such that the CCA end of one tRNA interacts with the anticodon of the symmetry-related tRNA. This provides us with a partial view of a codon-anticodon interaction and gives insights into the positioning of residue 37, and of its posttranscriptional modifications, relative to the first base of the codon.
The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop.,Benas P, Bec G, Keith G, Marquet R, Ehresmann C, Ehresmann B, Dumas P RNA. 2000 Oct;6(10):1347-55. PMID:11073212[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Benas P, Bec G, Keith G, Marquet R, Ehresmann C, Ehresmann B, Dumas P. The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop. RNA. 2000 Oct;6(10):1347-55. PMID:11073212
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