2qa4: Difference between revisions

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New page: left|200px {{Structure |PDB= 2qa4 |SIZE=350|CAPTION= <scene name='initialview01'>2qa4</scene>, resolution 3.0Å |SITE= <scene name='pdbsite=AC1:Mg+Binding+Site+Fo...
 
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[[Image:2qa4.jpg|left|200px]]


{{Structure
==A more complete structure of the the L7/L12 stalk of the Haloarcula marismortui 50S large ribosomal subunit==
|PDB= 2qa4 |SIZE=350|CAPTION= <scene name='initialview01'>2qa4</scene>, resolution 3.0&Aring;
<StructureSection load='2qa4' size='340' side='right'caption='[[2qa4]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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== Structural highlights ==
|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OMG:O2&#39;-METHYLGUANOSINE-5&#39;-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2&#39;-METHYLURIDINE+5&#39;-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5&#39;-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5&#39;-MONOPHOSHATE'>UR3</scene>
<table><tr><td colspan='2'>[[2qa4]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QA4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QA4 FirstGlance]. <br>
|ACTIVITY=
</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&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK01143 rpl11p], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd00349 Ribosomal_L11], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG0089 RplW], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK05518 rpl6p], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00347 Ribosomal_L6], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK01192 PRK01192], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG1727 RPL18A], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK04005 PRK04005], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK01191 rpl24p], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01418 Ribosomal_L19e_A], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK01242 rpl39e], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam01246 Ribosomal_L24e], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK08571 rpl14p], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK08569 rpl18p], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK04179 rpl37e], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00673 Ribosomal_L5_C], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK04219 rpl5p], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00281 Ribosomal_L5], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK12766 PRK12766], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01657 Ribosomal_L7], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK03976 rpl37ae], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00181 Ribosomal_L2], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK09612 rpl2p], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03947 Ribosomal_L2_C], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG0244 RplJ], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd00392 Ribosomal_L13], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK06419 rpl15p], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK04243 PRK04243], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd00336 Ribosomal_L22], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK04175 rpl7ae], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK04231 rpl3p], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00831 Ribosomal_L29], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK04199 rpl10e], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK04306 PRK04306], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK05767 rpl44e], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK04042 rpl4lp]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qa4 OCA], [https://pdbe.org/2qa4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qa4 RCSB], [https://www.ebi.ac.uk/pdbsum/2qa4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qa4 ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qa4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qa4 OCA], [http://www.ebi.ac.uk/pdbsum/2qa4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2qa4 RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qa/2qa4_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2qa4 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Initiation factors, elongation factors, and release factors all interact with the L7/L12 stalk of the large ribosomal subunit during their respective GTP-dependent cycles on the ribosome. Electron density corresponding to the stalk is not present in previous crystal structures of either 50 S subunits or 70 S ribosomes. We have now discovered conditions that result in a more ordered factor-binding center in the Haloarcula marismortui (H.ma) large ribosomal subunit crystals and consequently allows the visualization of the full-length L11, the N-terminal domain (NTD) of L10 and helices 43 and 44 of 23 S rRNA. The resulting model is currently the most complete reported structure of a L7/L12 stalk in the context of a ribosome. This region contains a series of intermolecular interfaces that are smaller than those typically seen in other ribonucleoprotein interactions within the 50 S subunit. Comparisons of the L11 NTD position between the current structure, which is has an NTD splayed out with respect to previous structures, and other structures of ribosomes in different functional states demonstrates a dynamic range of L11 NTD movements. We propose that the L11 NTD moves through three different relative positions during the translational cycle: apo-ribosome, factor-bound pre-GTP hydrolysis and post-GTP hydrolysis. These positions outline a pathway for L11 NTD movements that are dependent on the specific nucleotide state of the bound ligand. These three states are represented by the orientations of the L11 NTD relative to the ribosome and suggest that L11 may play a more specialized role in the factor binding cycle than previously appreciated.


'''A more complete structure of the the L7/L12 stalk of the Haloarcula marismortui 50S large ribosomal subunit'''
Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements.,Kavran JM, Steitz TA J Mol Biol. 2007 Aug 24;371(4):1047-59. Epub 2007 Jun 4. PMID:17599351<ref>PMID:17599351</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2qa4" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
Initiation factors, elongation factors, and release factors all interact with the L7/L12 stalk of the large ribosomal subunit during their respective GTP-dependent cycles on the ribosome. Electron density corresponding to the stalk is not present in previous crystal structures of either 50 S subunits or 70 S ribosomes. We have now discovered conditions that result in a more ordered factor-binding center in the Haloarcula marismortui (H.ma) large ribosomal subunit crystals and consequently allows the visualization of the full-length L11, the N-terminal domain (NTD) of L10 and helices 43 and 44 of 23 S rRNA. The resulting model is currently the most complete reported structure of a L7/L12 stalk in the context of a ribosome. This region contains a series of intermolecular interfaces that are smaller than those typically seen in other ribonucleoprotein interactions within the 50 S subunit. Comparisons of the L11 NTD position between the current structure, which is has an NTD splayed out with respect to previous structures, and other structures of ribosomes in different functional states demonstrates a dynamic range of L11 NTD movements. We propose that the L11 NTD moves through three different relative positions during the translational cycle: apo-ribosome, factor-bound pre-GTP hydrolysis and post-GTP hydrolysis. These positions outline a pathway for L11 NTD movements that are dependent on the specific nucleotide state of the bound ligand. These three states are represented by the orientations of the L11 NTD relative to the ribosome and suggest that L11 may play a more specialized role in the factor binding cycle than previously appreciated.
*[[Large Ribosomal Subunit of Haloarcula|Large Ribosomal Subunit of Haloarcula]]
 
*[[Ribosome 3D structures|Ribosome 3D structures]]
==About this Structure==
== References ==
2QA4 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QA4 OCA].
<references/>
 
__TOC__
==Reference==
</StructureSection>
Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements., Kavran JM, Steitz TA, J Mol Biol. 2007 Aug 24;371(4):1047-59. Epub 2007 Jun 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17599351 17599351]
[[Category: Haloarcula marismortui]]
[[Category: Haloarcula marismortui]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Kavran, J M.]]
[[Category: Kavran JM]]
[[Category: Steitz, T A.]]
[[Category: Steitz TA]]
[[Category: large ribosomal subunit]]
[[Category: metal-binding]]
[[Category: ribonucleoprotein]]
[[Category: ribosomal protein]]
[[Category: ribosome]]
[[Category: rna-binding]]
[[Category: rrna-binding]]
[[Category: trna-binding]]
[[Category: zinc]]
[[Category: zinc-finger]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  2 11:58:10 2008''

Latest revision as of 14:27, 30 August 2023

A more complete structure of the the L7/L12 stalk of the Haloarcula marismortui 50S large ribosomal subunitA more complete structure of the the L7/L12 stalk of the Haloarcula marismortui 50S large ribosomal subunit

Structural highlights

2qa4 is a 10 chain structure with sequence from Haloarcula marismortui. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3Å
Ligands:, , , , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL2_HALMA One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A]

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

Initiation factors, elongation factors, and release factors all interact with the L7/L12 stalk of the large ribosomal subunit during their respective GTP-dependent cycles on the ribosome. Electron density corresponding to the stalk is not present in previous crystal structures of either 50 S subunits or 70 S ribosomes. We have now discovered conditions that result in a more ordered factor-binding center in the Haloarcula marismortui (H.ma) large ribosomal subunit crystals and consequently allows the visualization of the full-length L11, the N-terminal domain (NTD) of L10 and helices 43 and 44 of 23 S rRNA. The resulting model is currently the most complete reported structure of a L7/L12 stalk in the context of a ribosome. This region contains a series of intermolecular interfaces that are smaller than those typically seen in other ribonucleoprotein interactions within the 50 S subunit. Comparisons of the L11 NTD position between the current structure, which is has an NTD splayed out with respect to previous structures, and other structures of ribosomes in different functional states demonstrates a dynamic range of L11 NTD movements. We propose that the L11 NTD moves through three different relative positions during the translational cycle: apo-ribosome, factor-bound pre-GTP hydrolysis and post-GTP hydrolysis. These positions outline a pathway for L11 NTD movements that are dependent on the specific nucleotide state of the bound ligand. These three states are represented by the orientations of the L11 NTD relative to the ribosome and suggest that L11 may play a more specialized role in the factor binding cycle than previously appreciated.

Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements.,Kavran JM, Steitz TA J Mol Biol. 2007 Aug 24;371(4):1047-59. Epub 2007 Jun 4. PMID:17599351[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Kavran JM, Steitz TA. Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements. J Mol Biol. 2007 Aug 24;371(4):1047-59. Epub 2007 Jun 4. PMID:17599351 doi:10.1016/j.jmb.2007.05.091

2qa4, resolution 3.00Å

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