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==Crystal structure of the 30S ribosome in complex with compound 39==
==Crystal structure of the 30S ribosome in complex with compound 39==
<StructureSection load='4b3t' size='340' side='right' caption='[[4b3t]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
<StructureSection load='4b3t' size='340' side='right'caption='[[4b3t]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4b3t]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus_hb8 Thermus thermophilus hb8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4B3T FirstGlance]. <br>
<table><tr><td colspan='2'>[[4b3t]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4B3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4B3T FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3TS:(2S,3S,4R,5R,6R)-2-(AMINOMETHYL)-5-AZANYL-6-[(2R,3S,4R,5S)-5-[(1R,2R,3S,5R,6S)-3,5-BIS(AZANYL)-2-[(2S,3R,4R,5S,6R)-3-AZANYL-5-[(4-CHLOROPHENYL)METHOXY]-6-(HYDROXYMETHYL)-4-OXIDANYL-OXAN-2-YL]OXY-6-OXIDANYL-CYCLOHEXYL]OXY-2-(HYDROXYMETHYL)-4-OXIDANYL-OXOLAN-3-YL]OXY-OXANE-3,4-DIOL'>3TS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4b3m|4b3m]], [[4b3r|4b3r]], [[4b3s|4b3s]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3TS:(2S,3S,4R,5R,6R)-2-(AMINOMETHYL)-5-AZANYL-6-[(2R,3S,4R,5S)-5-[(1R,2R,3S,5R,6S)-3,5-BIS(AZANYL)-2-[(2S,3R,4R,5S,6R)-3-AZANYL-5-[(4-CHLOROPHENYL)METHOXY]-6-(HYDROXYMETHYL)-4-OXIDANYL-OXAN-2-YL]OXY-6-OXIDANYL-CYCLOHEXYL]OXY-2-(HYDROXYMETHYL)-4-OXIDANYL-OXOLAN-3-YL]OXY-OXANE-3,4-DIOL'>3TS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b3t OCA], [http://pdbe.org/4b3t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4b3t RCSB], [http://www.ebi.ac.uk/pdbsum/4b3t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4b3t 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=4b3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4b3t OCA], [https://pdbe.org/4b3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4b3t RCSB], [https://www.ebi.ac.uk/pdbsum/4b3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4b3t ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] 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. [[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/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345]  Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [[http://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] [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] 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.[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] 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). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] 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 (By similarity).[HAMAP-Rule:MF_01343]  Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] 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 central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[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/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] 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. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]  
[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]
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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==See Also==
==See Also==
*[[Ribosomal protein THX|Ribosomal protein THX]]
*[[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 27: Line 27:
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Thermus thermophilus hb8]]
[[Category: Large Structures]]
[[Category: Akbergenov, R]]
[[Category: Thermus thermophilus HB8]]
[[Category: Bottger, E C]]
[[Category: Akbergenov R]]
[[Category: Boukari, H]]
[[Category: Bottger EC]]
[[Category: Duscha, S]]
[[Category: Boukari H]]
[[Category: Freihofer, P]]
[[Category: Duscha S]]
[[Category: Kudyba, I]]
[[Category: Freihofer P]]
[[Category: Lang, K]]
[[Category: Kudyba I]]
[[Category: Matt, T]]
[[Category: Lang K]]
[[Category: Meyer, M]]
[[Category: Matt T]]
[[Category: Nandurikar, R S]]
[[Category: Meyer M]]
[[Category: Ng, C L]]
[[Category: Nandurikar RS]]
[[Category: Patak, R]]
[[Category: Ng CL]]
[[Category: Perez-Fernandez, D]]
[[Category: Patak R]]
[[Category: Ramakrishnan, V]]
[[Category: Perez-Fernandez D]]
[[Category: Reddy, M S.K]]
[[Category: Ramakrishnan V]]
[[Category: Shcherbakov, D]]
[[Category: Reddy MSK]]
[[Category: Vasella, A]]
[[Category: Shcherbakov D]]
[[Category: Aminoglycoside]]
[[Category: Vasella A]]
[[Category: Antibiotic]]
[[Category: Ribosome]]

Latest revision as of 14:42, 20 December 2023

Crystal structure of the 30S ribosome in complex with compound 39Crystal structure of the 30S ribosome in complex with compound 39

Structural highlights

4b3t is a 10 chain structure with sequence from Thermus thermophilus HB8. 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]

Publication Abstract from PubMed

Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.

4'-O-substitutions determine selectivity of aminoglycoside antibiotics.,Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubbaka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Bottger EC Nat Commun. 2014 Jan 28;5:3112. doi: 10.1038/ncomms4112. PMID:24473108[1]

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

See Also

References

  1. ↑ Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubbaka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Bottger EC. 4'-O-substitutions determine selectivity of aminoglycoside antibiotics. Nat Commun. 2014 Jan 28;5:3112. doi: 10.1038/ncomms4112. PMID:24473108 doi:http://dx.doi.org/10.1038/ncomms4112

4b3t, resolution 3.00Å

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