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1dv4

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Revision as of 04:10, 30 August 2017

PARTIAL STRUCTURE OF 16S RNA OF THE SMALL RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS

Structural highlights

1dv4 is a 3 chain structure with sequence from Geobacillus stearothermophilus and Thermus thermophilus. This structure supersedes the now removed PDB entry 1c59. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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] [RS5_GEOSE] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).

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

The electron density map of the small ribosomal subunit from Thermus thermophilus, constructed at 4.5 A resolution, shows the recognizable morphology of this particle, as well as structural features that were interpreted as ribosomal RNA and proteins. Unbiased assignments, carried out by quantitative covalent binding of heavy atom compounds at predetermined sites, led to the localization of the surface of the ribosomal protein S13 at a position compatible with previous assignments, whereas the surface of S11 was localized at a distance of about twice its diameter from the site suggested for its center by neutron scattering. Proteins S5 and S7, whose structures have been determined crystallographically, were visually placed in the map with no alterations in their conformations. Regions suitable to host the fold of protein S15 were detected in several positions, all at a significant distance from the location of this protein in the neutron scattering map. Targeting the 16S RNA region, where mRNA docks to allow the formation of the initiation complex by a mercurated mRNA analog, led to the characterization of its vicinity.

The small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: pattern fittings and the identification of a functional site.,Tocilj A, Schlunzen F, Janell D, Gluhmann M, Hansen HA, Harms J, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14252-7. PMID:10588692^[1]

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

References

↑ Tocilj A, Schlunzen F, Janell D, Gluhmann M, Hansen HA, Harms J, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A. The small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: pattern fittings and the identification of a functional site. Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14252-7. PMID:10588692

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dv4"

@@ Line 1: / Line 1: @@
 ==PARTIAL STRUCTURE OF 16S RNA OF THE SMALL RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS==
 <StructureSection load='1dv4' size='340' side='right' caption='[[1dv4]], [[Resolution|resolution]] 4.50&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=WO2:OCTADECATUNGSTENYL+DIPHOSPHATE'>WO2</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene></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=1dv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv4 OCA], [http://pdbe.org/1dv4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dv4 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv4 PDBsum]</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=1dv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv4 OCA], [http://pdbe.org/1dv4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dv4 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv4 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 17: / Line 18: @@
     <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/chain_selection.php?pdb_ID=2ata 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=1dv4 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

1dv4

From Proteopedia

Revision as of 04:10, 30 August 2017

PARTIAL STRUCTURE OF 16S RNA OF THE SMALL RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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