1dfu: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
==CRYSTAL STRUCTURE OF E.COLI RIBOSOMAL PROTEIN L25 COMPLEXED WITH A 5S RRNA FRAGMENT AT 1.8 A RESOLUTION==
==CRYSTAL STRUCTURE OF E.COLI RIBOSOMAL PROTEIN L25 COMPLEXED WITH A 5S RRNA FRAGMENT AT 1.8 A RESOLUTION==
<StructureSection load='1dfu' size='340' side='right' caption='[[1dfu]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='1dfu' size='340' side='right'caption='[[1dfu]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1dfu]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DFU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DFU FirstGlance]. <br>
<table><tr><td colspan='2'>[[1dfu]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DFU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DFU 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></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]] 1.8&#8491;</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=1dfu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dfu OCA], [http://pdbe.org/1dfu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dfu RCSB], [http://www.ebi.ac.uk/pdbsum/1dfu PDBsum]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1dfu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dfu OCA], [https://pdbe.org/1dfu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dfu RCSB], [https://www.ebi.ac.uk/pdbsum/1dfu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dfu ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336]  
[https://www.uniprot.org/uniprot/RL25_ECOLI RL25_ECOLI] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/1dfu_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/1dfu_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
Line 18: Line 20:
</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=1dfu ConSurf].
</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=1dfu ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of Escherichia coli ribosomal protein L25 bound to an 18-base pair portion of 5S ribosomal RNA, which contains "loop E," has been determined at 1.8-A resolution. The protein primarily recognizes a unique RNA shape, although five side chains make direct or water-mediated interactions with bases. Three beta-strands lie in the widened minor groove of loop E formed by noncanonical base pairs and cross-strand purine stacks, and an alpha-helix interacts in an adjacent widened major groove. The structure of loop E is largely the same as that of uncomplexed RNA (rms deviation of 0.4 A for 11 base pairs), and 3 Mg(2+) ions that stabilize the noncanonical base pairs lie in the same or similar locations in both structures. Perhaps surprisingly, those residues interacting with the RNA backbone are the most conserved among known L25 sequences, whereas those interacting with the bases are not.
Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.,Lu M, Steitz TA Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2023-8. PMID:10696113<ref>PMID:10696113</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1dfu" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribosomal protein L25|Ribosomal protein L25]]
*[[Ribosomal protein L25|Ribosomal protein L25]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus coli migula 1895]]
[[Category: Escherichia coli]]
[[Category: Lu, M]]
[[Category: Large Structures]]
[[Category: Steitz, T A]]
[[Category: Lu M]]
[[Category: Protein-rna complex]]
[[Category: Steitz TA]]
[[Category: Ribosome]]

Latest revision as of 09:53, 7 February 2024

CRYSTAL STRUCTURE OF E.COLI RIBOSOMAL PROTEIN L25 COMPLEXED WITH A 5S RRNA FRAGMENT AT 1.8 A RESOLUTIONCRYSTAL STRUCTURE OF E.COLI RIBOSOMAL PROTEIN L25 COMPLEXED WITH A 5S RRNA FRAGMENT AT 1.8 A RESOLUTION

Structural highlights

1dfu is a 3 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.8Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL25_ECOLI This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. Binds to the 5S rRNA independently of L5 and L18. Not required for binding of the 5S rRNA/L5/L18 subcomplex to 23S rRNA.[HAMAP-Rule:MF_01336]

Evolutionary Conservation

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

See Also

1dfu, resolution 1.80Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1dfu&oldid=4041874"