1n32: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:


==Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position at the a site with paromomycin==
==Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position at the a site with paromomycin==
<StructureSection load='1n32' size='340' side='right' caption='[[1n32]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
<StructureSection load='1n32' size='340' side='right'caption='[[1n32]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1n32]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N32 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N32 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1n32]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N32 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N32 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=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1j5e|1j5e]], [[1fjg|1fjg]], [[1ibl|1ibl]], [[1ibk|1ibk]], [[1ibm|1ibm]], [[1n33|1n33]], [[1n34|1n34]], [[1n36|1n36]]</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=1n32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n32 OCA], [https://pdbe.org/1n32 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n32 RCSB], [https://www.ebi.ac.uk/pdbsum/1n32 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n32 ProSAT]</span></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=1n32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n32 OCA], [http://pdbe.org/1n32 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n32 RCSB], [http://www.ebi.ac.uk/pdbsum/1n32 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n32 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RS19_THETH RS19_THETH]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS5_THETH RS5_THETH]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B]  Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).[HAMAP-Rule:MF_01307_B] [[http://www.uniprot.org/uniprot/RS15_THETH RS15_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA.  Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS16_THETH RS16_THETH]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains. [[http://www.uniprot.org/uniprot/RSHX_THETH RSHX_THETH]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THETH RS14Z_THETH]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS10_THETH RS10_THETH]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS12_THETH RS12_THETH]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B]  Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RS6_THETH RS6_THETH]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS17_THETH RS17_THETH]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS8_THETH RS8_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity).
[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
== 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/n3/1n32_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n3/1n32_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
Line 32: Line 31:


==See Also==
==See Also==
*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
== References ==
Line 37: Line 37:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: IV, F V.Murphy]]
[[Category: Murphy IV FV]]
[[Category: Ogle, J M]]
[[Category: Ogle JM]]
[[Category: Ramakrishnan, V]]
[[Category: Ramakrishnan V]]
[[Category: Tarry, M J]]
[[Category: Tarry MJ]]
[[Category: 30s ribosomal subunit]]
[[Category: A site]]
[[Category: Antibiotic]]
[[Category: Anticodon]]
[[Category: Codon]]
[[Category: Decoding]]
[[Category: G:u]]
[[Category: Gu]]
[[Category: Messenger rna]]
[[Category: Mismatch]]
[[Category: Mrna]]
[[Category: Near-cognate]]
[[Category: Paromomycin]]
[[Category: Ribosome]]
[[Category: Stem-loop]]
[[Category: Transfer rna]]
[[Category: Trna]]
[[Category: Wobble]]

Latest revision as of 10:03, 30 October 2024

Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position at the a site with paromomycinStructure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position at the a site with paromomycin

Structural highlights

1n32 is a 10 chain structure with sequence from Thermus thermophilus. 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

RS2_THET8 Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]

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

A structural and mechanistic explanation for the selection of tRNAs by the ribosome has been elusive. Here, we report crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at the decoding center and compare affinities of equivalent complexes in solution. In ribosomal interactions with near-cognate tRNA, deviation from Watson-Crick geometry results in uncompensated desolvation of hydrogen-bonding partners at the codon-anticodon minor groove. As a result, the transition to a closed form of the 30S induced by cognate tRNA is unfavorable for near-cognate tRNA unless paromomycin induces part of the rearrangement. We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity.

Selection of tRNA by the ribosome requires a transition from an open to a closed form.,Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V Cell. 2002 Nov 27;111(5):721-32. PMID:12464183[1]

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

See Also

References

  1. ↑ Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell. 2002 Nov 27;111(5):721-32. PMID:12464183

1n32, resolution 3.00Å

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=1n32&oldid=4199787"