4zer: Difference between revisions

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-'''Unreleased structure'''
-The entry 4zer is ON HOLD
+==Crystal structure of the Onc112 antimicrobial peptide bound to the Thermus thermophilus 70S ribosome==
+<StructureSection load='4zer' size='340' side='right'caption='[[4zer]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4zer]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Oncopeltus_fasciatus Oncopeltus fasciatus] and [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=4ZER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZER FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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'>[https://proteopedia.org/fgij/fg.htm?mol=4zer FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zer OCA], [https://pdbe.org/4zer PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zer RCSB], [https://www.ebi.ac.uk/pdbsum/4zer PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zer ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL24_THET8 RL24_THET8] 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 (By similarity).[HAMAP-Rule:MF_01326_B]  One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_B]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The increasing prevalence of multidrug-resistant pathogenic bacteria is making current antibiotics obsolete. Proline-rich antimicrobial peptides (PrAMPs) display potent activity against Gram-negative bacteria and thus represent an avenue for antibiotic development. PrAMPs from the oncocin family interact with the ribosome to inhibit translation, but their mode of action has remained unclear. Here we have determined a structure of the Onc112 peptide in complex with the Thermus thermophilus 70S ribosome at a resolution of 3.1 A by X-ray crystallography. The Onc112 peptide binds within the ribosomal exit tunnel and extends toward the peptidyl transferase center, where it overlaps with the binding site for an aminoacyl-tRNA. We show biochemically that the binding of Onc112 blocks and destabilizes the initiation complex, thus preventing entry into the elongation phase. Our findings provide a basis for the future development of this class of potent antimicrobial agents.
-Authors: Seefeldt, A.C., Perebaskine, N., Innis, C.A.
+The proline-rich antimicrobial peptide Onc112 inhibits translation by blocking and destabilizing the initiation complex.,Seefeldt AC, Nguyen F, Antunes S, Perebaskine N, Graf M, Arenz S, Inampudi KK, Douat C, Guichard G, Wilson DN, Innis CA Nat Struct Mol Biol. 2015 May 18. doi: 10.1038/nsmb.3034. PMID:25984971<ref>PMID:25984971</ref>
-Description: Crystal structure of Onc112 antimicrobial peptide bound to the Thermus thermophilus 70S ribosome
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Seefeldt, A.C]]
+<div class="pdbe-citations 4zer" style="background-color:#fffaf0;"></div>
-[[Category: Innis, C.A]]
-[[Category: Perebaskine, N]]
+==See Also==
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Oncopeltus fasciatus]]
+[[Category: Thermus thermophilus HB8]]
+[[Category: Antunes S]]
+[[Category: Arenz S]]
+[[Category: Douat C]]
+[[Category: Graf M]]
+[[Category: Guichard G]]
+[[Category: Inampudi KK]]
+[[Category: Innis CA]]
+[[Category: Nguyen F]]
+[[Category: Perebaskine N]]
+[[Category: Seefeldt AC]]
+[[Category: Wilson DN]]