1eg0: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 3: Line 3:
<SX load='1eg0' size='340' side='right' viewer='molstar' caption='[[1eg0]], [[Resolution|resolution]] 11.50&Aring;' scene=''>
<SX load='1eg0' size='340' side='right' viewer='molstar' caption='[[1eg0]], [[Resolution|resolution]] 11.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1eg0]] is a 15 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=1EG0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EG0 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1eg0]] is a 10 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=1EG0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EG0 FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 11.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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=1eg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eg0 OCA], [https://pdbe.org/1eg0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eg0 RCSB], [https://www.ebi.ac.uk/pdbsum/1eg0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eg0 ProSAT]</span></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=1eg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eg0 OCA], [https://pdbe.org/1eg0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eg0 RCSB], [https://www.ebi.ac.uk/pdbsum/1eg0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eg0 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RS5_GEOSE 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). [[https://www.uniprot.org/uniprot/RS17_GEOSE RS17_GEOSE]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.[HAMAP-Rule:MF_01345] [[https://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). [[https://www.uniprot.org/uniprot/RL11_THEMA RL11_THEMA]] This protein binds directly to 23S ribosomal RNA. [[https://www.uniprot.org/uniprot/RL6_GEOSE RL6_GEOSE]] It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center (By similarity). This protein binds to the 23S rRNA, and is important in its secondary structure.[HAMAP-Rule:MF_01365] [[https://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] [[https://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). [[https://www.uniprot.org/uniprot/RL1_THETH RL1_THETH]] The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release (By similarity). Binds directly to 23S rRNA.[HAMAP-Rule:MF_01318] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (By similarity).[HAMAP-Rule:MF_01318] [[https://www.uniprot.org/uniprot/RS4_GEOSE RS4_GEOSE]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit (By similarity).[HAMAP-Rule:MF_01306_B]  With S5 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01306_B]
[https://www.uniprot.org/uniprot/RS4_BACSU RS4_BACSU] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy; many suppressors of streptomycin-dependent mutants of protein S12 are found in this protein, some but not all of which decrease translational accuracy (ram, ribosomal ambiguity mutations).  S4 represses its own expression; it is not know if this is at the level of translation or of mRNA stability.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 19: 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=1eg0 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=1eg0 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map of the complex. This map allows identification of RNA helices, peripheral proteins, and intersubunit bridges. Comparison of double-stranded RNA regions and positions of proteins identified in both cryo-EM and X-ray maps indicates good overall agreement but points to rearrangements of ribosomal components required for the subunit association. Fitting of known components of the 50S stalk base region into the map defines the architecture of the GTPase-associated center and reveals a major change in the orientation of the alpha-sarcin-ricin loop. Analysis of the bridging connections between the subunits provides insight into the dynamic signaling mechanism between the ribosomal subunits.
Solution structure of the E. coli 70S ribosome at 11.5 A resolution.,Gabashvili IS, Agrawal RK, Spahn CM, Grassucci RA, Svergun DI, Frank J, Penczek P Cell. 2000 Mar 3;100(5):537-49. PMID:10721991<ref>PMID:10721991</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1eg0" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribosomal protein L11|Ribosomal protein L11]]
*[[Ribosomal protein L11 3D structures|Ribosomal protein L11 3D structures]]
*[[Ribosomal protein L6|Ribosomal protein L6]]
*[[Ribosomal protein L6|Ribosomal protein L6]]
== References ==
<references/>
__TOC__
__TOC__
</SX>
</SX>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Agrawal, R K]]
[[Category: Agrawal RK]]
[[Category: Frank, J]]
[[Category: Frank J]]
[[Category: Gabashvili, I S]]
[[Category: Gabashvili IS]]
[[Category: Grassucci, R A]]
[[Category: Grassucci RA]]
[[Category: Penczek, P]]
[[Category: Penczek P]]
[[Category: Spahn, C M.T]]
[[Category: Spahn CMT]]
[[Category: Svergun, D I]]
[[Category: Svergun DI]]
[[Category: 70s ribosome]]
[[Category: Low resolution model]]
[[Category: Ribosome]]

Latest revision as of 10:02, 7 February 2024

FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOMEFITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME

1eg0, resolution 11.50Å

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=1eg0&oldid=4042522"