1nt2: Difference between revisions

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[[Image:1nt2.jpg|left|200px]]


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==CRYSTAL STRUCTURE OF FIBRILLARIN/NOP5P COMPLEX==
The line below this paragraph, containing "STRUCTURE_1nt2", creates the "Structure Box" on the page.
<StructureSection load='1nt2' size='340' side='right'caption='[[1nt2]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1nt2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NT2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NT2 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
{{STRUCTURE_1nt2|  PDB=1nt2  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nt2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nt2 OCA], [https://pdbe.org/1nt2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nt2 RCSB], [https://www.ebi.ac.uk/pdbsum/1nt2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nt2 ProSAT]</span></td></tr>
 
</table>
'''CRYSTAL STRUCTURE OF FIBRILLARIN/NOP5P COMPLEX'''
== Function ==
 
[https://www.uniprot.org/uniprot/FLPA_ARCFU FLPA_ARCFU] Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA.<ref>PMID:15286083</ref>
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
Nop56p and Nop58p are two core proteins of the box C/D snoRNPs that interact concurrently with fibrillarin and snoRNAs to function in enzyme assembly and catalysis. Here we report the 2.9 A resolution co-crystal structure of an archaeal homolog of Nop56p/Nop58p, Nop5p, in complex with fibrillarin from Archaeoglobus fulgidus (AF) and the methyl donor S-adenosyl-L-methionine. The N-terminal domain of Nop5p forms a complementary surface to fibrillarin that serves to anchor the catalytic subunit and to stabilize cofactor binding. A coiled coil in Nop5p mediates dimerization of two fibrillarin-Nop5p heterodimers for optimal interactions with bipartite box C/D RNAs. Structural analysis and complementary biochemical data demonstrate that the conserved C-terminal domain of Nop5p harbors RNA-binding sites. A model of box C/D snoRNP assembly is proposed based on the presented structural and biochemical data.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nt/1nt2_consurf.spt"</scriptWhenChecked>
1NT2 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NT2 OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
Structure and function of archaeal box C/D sRNP core proteins., Aittaleb M, Rashid R, Chen Q, Palmer JR, Daniels CJ, Li H, Nat Struct Biol. 2003 Apr;10(4):256-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12598892 12598892]
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1nt2 ConSurf].
[[Category: Archaeoglobus fulgidus]]
<div style="clear:both"></div>
[[Category: Protein complex]]
== References ==
[[Category: Aittaleb, M.]]
<references/>
[[Category: Chen, Q.]]
__TOC__
[[Category: Daniels, C J.]]
</StructureSection>
[[Category: Li, H.]]
[[Category: Archaeoglobus fulgidus DSM 4304]]
[[Category: Palmer, J R.]]
[[Category: Large Structures]]
[[Category: Rashid, R.]]
[[Category: Aittaleb M]]
[[Category: Ademet]]
[[Category: Chen Q]]
[[Category: Binding motif]]
[[Category: Daniels CJ]]
[[Category: Coiled coil]]
[[Category: Li H]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 02:56:39 2008''
[[Category: Palmer JR]]
[[Category: Rashid R]]

Latest revision as of 10:59, 14 February 2024

CRYSTAL STRUCTURE OF FIBRILLARIN/NOP5P COMPLEXCRYSTAL STRUCTURE OF FIBRILLARIN/NOP5P COMPLEX

Structural highlights

1nt2 is a 2 chain structure with sequence from Archaeoglobus fulgidus DSM 4304. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.9Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FLPA_ARCFU Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA.[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

  1. ↑ Aittaleb M, Visone T, Fenley MO, Li H. Structural and thermodynamic evidence for a stabilizing role of Nop5p in S-adenosyl-L-methionine binding to fibrillarin. J Biol Chem. 2004 Oct 1;279(40):41822-9. Epub 2004 Jul 30. PMID:15286083 doi:http://dx.doi.org/10.1074/jbc.M406209200

1nt2, resolution 2.90Å

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