View source for 6spf


==Pseudomonas aeruginosa 70s ribosome from an aminoglycoside resistant clinical isolate==
<StructureSection load='6spf' size='340' side='right'caption='[[6spf]], [[Resolution|resolution]] 2.89&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6spf]] is a 53 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SPF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SPF FirstGlance]. <br>
</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=6spf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6spf OCA], [http://pdbe.org/6spf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6spf RCSB], [http://www.ebi.ac.uk/pdbsum/6spf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6spf ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/E2RXT7_PSEAI E2RXT7_PSEAI]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326]  One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/A0A2V3F3S9_PSEAI A0A2V3F3S9_PSEAI]] This protein binds to the 23S rRNA, and is important in its secondary structure. 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.[HAMAP-Rule:MF_01365][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/A0A069QEE3_PSEAI A0A069QEE3_PSEAI]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit.[HAMAP-Rule:MF_00382][RuleBase:RU000560] [[http://www.uniprot.org/uniprot/A0A072ZDZ0_PSEAI A0A072ZDZ0_PSEAI]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00352917] [[http://www.uniprot.org/uniprot/A0A263PZC6_PSEAI A0A263PZC6_PSEAI]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/A0A071L394_PSEAI A0A071L394_PSEAI]] 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.[HAMAP-Rule:MF_00403][RuleBase:RU003623]  With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403][RuleBase:RU003623] [[http://www.uniprot.org/uniprot/A0A072ZJG4_PSEAI A0A072ZJG4_PSEAI]] Binds the 23S rRNA.[HAMAP-Rule:MF_00501][SAAS:SAAS00804277] [[http://www.uniprot.org/uniprot/E2RXT9_PSEAI E2RXT9_PSEAI]] 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.[HAMAP-Rule:MF_01302] [[http://www.uniprot.org/uniprot/E2RXT1_PSEAI E2RXT1_PSEAI]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/E2RXT5_PSEAI E2RXT5_PSEAI]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/A0A071L356_PSEAI A0A071L356_PSEAI]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366][RuleBase:RU003878][SAAS:SAAS00725369] [[http://www.uniprot.org/uniprot/A0A140S919_PSEAI A0A140S919_PSEAI]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309] [[http://www.uniprot.org/uniprot/E2RXT6_PSEAI E2RXT6_PSEAI]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/E2RXT0_PSEAI E2RXT0_PSEAI]] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/A0A072ZBM5_PSEAI A0A072ZBM5_PSEAI]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01334][SAAS:SAAS00720025] [[http://www.uniprot.org/uniprot/E2RXT8_PSEAI E2RXT8_PSEAI]] 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.[HAMAP-Rule:MF_00537] [[http://www.uniprot.org/uniprot/A0A069QEB6_PSEAI A0A069QEB6_PSEAI]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342][RuleBase:RU004414] [[http://www.uniprot.org/uniprot/A0A072ZMU2_PSEAI A0A072ZMU2_PSEAI]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333] [[http://www.uniprot.org/uniprot/A0A2V3DLV3_PSEAI A0A2V3DLV3_PSEAI]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/A0A2V3F2U6_PSEAI A0A2V3F2U6_PSEAI]] One of the primary rRNA binding proteins, it binds directly to 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, probably blocks exit of the E-site tRNA.[HAMAP-Rule:MF_00480] [[http://www.uniprot.org/uniprot/A0A072ZDF7_PSEAI A0A072ZDF7_PSEAI]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.[HAMAP-Rule:MF_01306]  With S5 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01306] [[http://www.uniprot.org/uniprot/A0A241XHA2_PSEAI A0A241XHA2_PSEAI]] 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.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/E2RXT2_PSEAI E2RXT2_PSEAI]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/A0A2V3GYK0_PSEAI A0A2V3GYK0_PSEAI]] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS00731150] [[http://www.uniprot.org/uniprot/A0A2V3D5Z8_PSEAI A0A2V3D5Z8_PSEAI]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00124822] [[http://www.uniprot.org/uniprot/A0A071L3R7_PSEAI A0A071L3R7_PSEAI]] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343]  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.[HAMAP-Rule:MF_01343][RuleBase:RU004524] [[http://www.uniprot.org/uniprot/E2RXU0_PSEAI E2RXU0_PSEAI]] This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/A0A072ZDZ9_PSEAI A0A072ZDZ9_PSEAI]] Binds directly to 16S ribosomal RNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/A0A069Q263_PSEAI A0A069Q263_PSEAI]] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360][SAAS:SAAS00348112] [[http://www.uniprot.org/uniprot/A0A072ZKF0_PSEAI A0A072ZKF0_PSEAI]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/A0A072ZBZ2_PSEAI A0A072ZBZ2_PSEAI]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325][RuleBase:RU003906] [[http://www.uniprot.org/uniprot/E2RXU3_PSEAI E2RXU3_PSEAI]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/A0A241XG65_PSEAI A0A241XG65_PSEAI]] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.[HAMAP-Rule:MF_01307][SAAS:SAAS00085417]  With S4 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01307][SAAS:SAAS00085429] [[http://www.uniprot.org/uniprot/E2RXU4_PSEAI E2RXU4_PSEAI]] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/A0A1C7BCP0_PSEAI A0A1C7BCP0_PSEAI]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome.[HAMAP-Rule:MF_01331]  This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g., L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331][RuleBase:RU004008] [[http://www.uniprot.org/uniprot/A0A241XH26_PSEAI A0A241XH26_PSEAI]] Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328]  One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01328] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Resistance to antibiotics has become a major threat to modern medicine. The ribosome plays a fundamental role in cell vitality by the translation of the genetic code into proteins; hence, it is a major target for clinically useful antibiotics. We report here the cryo-electron microscopy structures of the ribosome of a pathogenic aminoglycoside (AG)-resistant Pseudomonas aeruginosa strain, as well as of a nonresistance strain isolated from a cystic fibrosis patient. The structural studies disclosed defective ribosome complex formation due to a conformational change of rRNA helix H69, an essential intersubunit bridge, and a secondary binding site of the AGs. In addition, a stable conformation of nucleotides A1486 and A1487, pointing into helix h44, is created compared to a non-AG-bound ribosome. We suggest that altering the conformations of ribosomal protein uL6 and rRNA helix H69, which interact with initiation-factor IF2, interferes with proper protein synthesis initiation.

Structure of Pseudomonas aeruginosa ribosomes from an aminoglycoside-resistant clinical isolate.,Halfon Y, Jimenez-Fernandez A, La Rosa R, Espinosa Portero R, Krogh Johansen H, Matzov D, Eyal Z, Bashan A, Zimmerman E, Belousoff M, Molin S, Yonath A Proc Natl Acad Sci U S A. 2019 Oct 14. pii: 1909831116. doi:, 10.1073/pnas.1909831116. PMID:31611393<ref>PMID:31611393</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6spf" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Bashan, A]]
[[Category: Belousoff, M]]
[[Category: Espinos, R]]
[[Category: Eyal, Z]]
[[Category: Halfon, Y]]
[[Category: Jimenez-Fernande, A]]
[[Category: Johansen, H Krogh]]
[[Category: Matzov, D]]
[[Category: Molin, S]]
[[Category: Ros, R La]]
[[Category: Yonath, A]]
[[Category: Zimmerman, E]]
[[Category: Ribosome]]