1m5l: Difference between revisions
No edit summary |
No edit summary |
||
| Line 4: | Line 4: | ||
|PDB= 1m5l |SIZE=350|CAPTION= <scene name='initialview01'>1m5l</scene> | |PDB= 1m5l |SIZE=350|CAPTION= <scene name='initialview01'>1m5l</scene> | ||
|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5l OCA], [http://www.ebi.ac.uk/pdbsum/1m5l PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1m5l RCSB]</span> | |||
}} | }} | ||
| Line 32: | Line 35: | ||
[[Category: sl-1]] | [[Category: sl-1]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:11:37 2008'' | ||
Revision as of 19:11, 30 March 2008
| |||||||||||||
| 1m5l | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ligands: | A, C, G, U | ||||||||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Structure of wild-type and mutant internal loops from the SL-1 domain of the HIV-1 packaging signal
Overview
The packaging signal (Psi) of the human immunodeficiency virus type 1 (HIV-1) enables encapsidation of the full-length genomic RNA against a background of a vast excess of cellular mRNAs. The core HIV-1 Psi is approximately 109 nucleotides and contains sequences critical for viral genomic dimerisation and splicing, in addition to the packaging signal. It consists of a series of stem-loops (termed SL-1 to SL-4), which can be arranged in a cloverleaf secondary structure. Using a combination of NMR spectroscopy, UV melting experiments, molecular modeling and phylogenetic analyses, we have explored the structure of two conserved internal loops proximal to the palindromic sequence of SL-1. Internal loop A, composed of six purines, forms a flexible structure that is strikingly similar to the Rev responsive element motif when bound to Rev protein. This result suggests that it may function as a protein-binding site. The absolutely conserved four-purine internal loop B is instead conformationally and thermodynamically unstable, and exhibits multiple conformations in solution. By introducing a double AGG to GGA mutation within this loop, its conformation is stabilised to form a new intra-molecular G:A:G base-triplet. The structure of the GGA mutant explains the relative instability of the wild-type loop. In a manner analogous to SL-3, we propose that conformational flexibility at this site may facilitate melting of the structure during Gag protein capture or genomic RNA dimerisation.
About this Structure
1M5L is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure and stability of wild-type and mutant RNA internal loops from the SL-1 domain of the HIV-1 packaging signal., Greatorex J, Gallego J, Varani G, Lever A, J Mol Biol. 2002 Sep 20;322(3):543-57. PMID:12225748
Page seeded by OCA on Sun Mar 30 22:11:37 2008
