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6v3e

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Cryo-EM structure of the Acinetobacter baumannii Ribosome: 30S subunit

6v3e, resolution 4.40Å

Structural highlights

6v3e is a 20 chain structure with sequence from Acinetobacter baumannii, Acinetobacter baumannii (strain ab0057), Acinetobacter sp. 263903-1, Acinetobacter sp. anc 5600 and Acinetobacter venetianus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RS6_ACIB5] Binds together with S18 to 16S ribosomal RNA. [A0A062C259_9GAMM] 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] [V5V9N0_ACIBA] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309] [RS7_ACIB5] 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. [RS17_ACIB5] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [RS12_ACIB5] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403] 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] [RS20_ACIB5] Binds directly to 16S ribosomal RNA. [RS15_ACIB5] 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. [RS14_ACIB5] 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. [RS8_ACIB5] 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. [RS4_ACIB5] 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. [A0A150HZL5_9GAMM] 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] [RS19_ACIB5] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [A0A1T1GZ10_9GAMM] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508] [RS13_ACIB5] 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. [RS5_ACIB5] With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.

Publication Abstract from PubMed

Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is Acinetobacter baumannii, a Gram-negative opportunistic pathogen that exhibits the remarkable ability to resist antibiotics through multiple mechanisms. As bacterial ribosomes represent a target for multiple distinct classes of existing antimicrobial agents, we here use single-particle cryo-electron microscopy (cryo-EM) to elucidate five different structural states of the A. baumannii ribosome, including the 70S, 50S, and 30S forms. We also determined interparticle motions of the 70S ribosome in different tRNA bound states using three-dimensional (3D) variability analysis. Together, our structural data further our understanding of the ribosome from A. baumannii and other Gram-negative pathogens and will enable structure-based drug discovery to combat antibiotic-resistant bacterial infections.IMPORTANCE Acinetobacter baumannii is a severe nosocomial threat largely due to its intrinsic antibiotic resistance and remarkable ability to acquire new resistance determinants. The bacterial ribosome serves as a major target for modern antibiotics and the design of new therapeutics. Here, we present cryo-EM structures of the A. baumannii 70S ribosome, revealing several unique species-specific structural features that may facilitate future drug development to combat this recalcitrant bacterial pathogen.

Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development.,Morgan CE, Huang W, Rudin SD, Taylor DJ, Kirby JE, Bonomo RA, Yu EW mBio. 2020 Jan 21;11(1). pii: mBio.03117-19. doi: 10.1128/mBio.03117-19. PMID:31964740^[1]

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

References

↑ Morgan CE, Huang W, Rudin SD, Taylor DJ, Kirby JE, Bonomo RA, Yu EW. Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development. mBio. 2020 Jan 21;11(1). pii: mBio.03117-19. doi: 10.1128/mBio.03117-19. PMID:31964740 doi:http://dx.doi.org/10.1128/mBio.03117-19

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6v3e"

@@ Line 3: / Line 3: @@
 <SX load='6v3e' size='340' side='right' viewer='molstar' caption='[[6v3e]], [[Resolution|resolution]] 4.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6v3e]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii], [http://en.wikipedia.org/wiki/Acinetobacter_baumannii_(strain_ab0057) Acinetobacter baumannii (strain ab0057)], [http://en.wikipedia.org/wiki/Acinetobacter_sp._263903-1 Acinetobacter sp. 263903-1], [http://en.wikipedia.org/wiki/Acinetobacter_sp._anc_5600 Acinetobacter sp. anc 5600] and [http://en.wikipedia.org/wiki/Acinetobacter_venetianus Acinetobacter venetianus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V3E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6V3E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6v3e]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii], [http://en.wikipedia.org/wiki/Acinetobacter_baumannii_(strain_ab0057) Acinetobacter baumannii (strain ab0057)], [http://en.wikipedia.org/wiki/Acinetobacter_sp._263903-1 Acinetobacter sp. 263903-1], [http://en.wikipedia.org/wiki/Acinetobacter_sp._anc_5600 Acinetobacter sp. anc 5600] and [http://en.wikipedia.org/wiki/Acinetobacter_venetianus Acinetobacter venetianus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V3E OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V3E FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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=6v3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v3e OCA], [http://pdbe.org/6v3e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v3e RCSB], [http://www.ebi.ac.uk/pdbsum/6v3e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v3e ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6v3e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v3e OCA], [http://pdbe.org/6v3e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v3e RCSB], [http://www.ebi.ac.uk/pdbsum/6v3e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v3e ProSAT]</span></td></tr>
 </table>
 == Function ==

6v3e

From Proteopedia

Current revision

Cryo-EM structure of the Acinetobacter baumannii Ribosome: 30S subunit

Structural highlights

Function

Publication Abstract from PubMed

References

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