3g6e

From Proteopedia

(Difference between revisions)

Current revision

Co-crystal structure of Homoharringtonine bound to the large ribosomal subunit

Structural highlights

3g6e is a 10 chain structure with sequence from Haloarcula marismortui. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:	, , , , , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL2_HALMA 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 (By similarity).[HAMAP-Rule:MF_01320_A]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 A. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.,Gurel G, Blaha G, Moore PB, Steitz TA J Mol Biol. 2009 May 29;389(1):146-56. Epub 2009 Apr 9. PMID:19362093^[1]

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

References

↑ Gurel G, Blaha G, Moore PB, Steitz TA. U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome. J Mol Biol. 2009 May 29;389(1):146-56. Epub 2009 Apr 9. PMID:19362093 doi:10.1016/j.jmb.2009.04.005

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3g6e"

@@ Line 1: / Line 1: @@
-[[Image:3g6e.png|left|200px]]
-<!--
+==Co-crystal structure of Homoharringtonine bound to the large ribosomal subunit==
-The line below this paragraph, containing "STRUCTURE_3g6e", creates the "Structure Box" on the page.
+<StructureSection load='3g6e' size='340' side='right'caption='[[3g6e]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3g6e]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G6E FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=HMT:(3BETA)-O~3~-[(2R)-2,6-DIHYDROXY-2-(2-METHOXY-2-OXOETHYL)-6-METHYLHEPTANOYL]CEPHALOTAXINE'>HMT</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
-{{STRUCTURE_3g6e|  PDB=3g6e  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3g6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g6e OCA], [https://pdbe.org/3g6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g6e RCSB], [https://www.ebi.ac.uk/pdbsum/3g6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g6e ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA] 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 (By similarity).[HAMAP-Rule:MF_01320_A]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g6/3g6e_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=3g6e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 A. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.
-===Co-crystal structure of Homoharringtonine bound to the large ribosomal subunit===
+U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.,Gurel G, Blaha G, Moore PB, Steitz TA J Mol Biol. 2009 May 29;389(1):146-56. Epub 2009 Apr 9. PMID:19362093<ref>PMID:19362093</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_19362093}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3g6e" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19362093 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19362093}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3g6e]] is a 30 chain structure of [[Ribosomal protein L10]], [[Ribosomal protein L2]], [[Ribosomal protein L3]], [[Ribosomal protein L4]], [[Ribosomal protein L5]], [[Ribosomal protein L6]] and [[Ribosomal protein L7]] with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3G6E OCA].
-==See Also==
-*[[Ribosomal protein L10]]
-*[[Ribosomal protein L2]]
-*[[Ribosomal protein L3]]
-*[[Ribosomal protein L4]]
-*[[Ribosomal protein L5]]
-*[[Ribosomal protein L6]]
-*[[Ribosomal protein L7]]
-==Reference==
-<ref group="xtra">PMID:19362093</ref><references group="xtra"/>
-[[Category: Haloarcula marismortui]]
-[[Category: Blaha, G.]]
-[[Category: Gurel, G.]]
-[[Category: Moore, P B.]]
-[[Category: Steitz, T A.]]
-[[Category: Acetylation]]
-[[Category: Antibiotic specificity]]
 [[Category: Haloarcula marismortui]]
-[[Category: Homoharringtonine]]
+[[Category: Large Structures]]
-[[Category: Large ribosomal subunit]]
+[[Category: Blaha G]]
-[[Category: Metal-binding]]
+[[Category: Gurel G]]
-[[Category: Ribonucleoprotein]]
+[[Category: Moore PB]]
-[[Category: Ribosomal protein]]
+[[Category: Steitz TA]]
-[[Category: Ribosome]]
-[[Category: Rna-binding]]
-[[Category: Rrna-binding]]
-[[Category: Trna-binding]]
-[[Category: Zinc]]
-[[Category: Zinc-finger]]

3g6e

From Proteopedia

Current revision

Co-crystal structure of Homoharringtonine bound to the large ribosomal subunit

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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