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4wqu

From Proteopedia

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Current revision

Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation factor G trapped by the antibiotic dityromycin

Structural highlights

4wqu is a 20 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 2.8Å
Ligands:	, , , , , , , , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL1_THET8 Directly binds to 23S rRNA. Forms what is known as the L1 stalk, which protrudes beyond the 70S ribosome surface. The stalk is preferentially stabilized in 70S versus 50S crystals. Interacts with the E site tRNA, blocking the exit path. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_01318_B] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (By similarity).[HAMAP-Rule:MF_01318_B]

Publication Abstract from PubMed

The universally conserved GTPase elongation factor G (EF-G) catalyzes the translocation of tRNA and mRNA on the ribosome after peptide bond formation. Despite numerous studies suggesting that EF-G undergoes extensive conformational rearrangements during translocation, high-resolution structures exist for essentially only one conformation of EF-G in complex with the ribosome. Here, we report four atomic-resolution crystal structures of EF-G bound to the ribosome programmed in the pre- and posttranslocational states and to the ribosome trapped by the antibiotic dityromycin. We observe a previously unseen conformation of EF-G in the pretranslocation complex, which is independently captured by dityromycin on the ribosome. Our structures provide insights into the conformational space that EF-G samples on the ribosome and reveal that tRNA translocation on the ribosome is facilitated by a structural transition of EF-G from a compact to an elongated conformation, which can be prevented by the antibiotic dityromycin.

Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation.,Lin J, Gagnon MG, Bulkley D, Steitz TA Cell. 2015 Jan 15;160(1-2):219-27. doi: 10.1016/j.cell.2014.11.049. PMID:25594181^[1]

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

References

↑ Lin J, Gagnon MG, Bulkley D, Steitz TA. Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation. Cell. 2015 Jan 15;160(1-2):219-27. doi: 10.1016/j.cell.2014.11.049. PMID:25594181 doi:http://dx.doi.org/10.1016/j.cell.2014.11.049

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4wqu"

Categories: Large Structures | Thermus thermophilus HB8 | Gagnon MG | Lin J | Steitz TA

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4wqu]] is a 20 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=4WQU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WQU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=004:(2S)-AMINO(PHENYL)ETHANOIC+ACID'>004</scene>, <scene name='pdbligand=2QY:(2Z)-3-(4-HYDROXYPHENYL)-2-(METHYLAMINO)PROP-2-ENOIC+ACID'>2QY</scene>, <scene name='pdbligand=2QZ:N,N-DIMETHYL-L-THREONINE'>2QZ</scene>, <scene name='pdbligand=2R1:(2E)-2-AMINO-4-HYDROXY-3-[(2R)-OXIRAN-2-YL]BUT-2-ENOIC+ACID'>2R1</scene>, <scene name='pdbligand=2R3:(BETAR)-BETA-HYDROXY-O-METHYL-L-TYROSINE'>2R3</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=004:(2S)-AMINO(PHENYL)ETHANOIC+ACID'>004</scene>, <scene name='pdbligand=2QY:(2Z)-3-(4-HYDROXYPHENYL)-2-(METHYLAMINO)PROP-2-ENOIC+ACID'>2QY</scene>, <scene name='pdbligand=2QZ:N,N-DIMETHYL-L-THREONINE'>2QZ</scene>, <scene name='pdbligand=2R1:(2E)-2-AMINO-4-HYDROXY-3-[(2R)-OXIRAN-2-YL]BUT-2-ENOIC+ACID'>2R1</scene>, <scene name='pdbligand=2R3:(BETAR)-BETA-HYDROXY-O-METHYL-L-TYROSINE'>2R3</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=MVA:N-METHYLVALINE'>MVA</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=4wqu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wqu OCA], [https://pdbe.org/4wqu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wqu RCSB], [https://www.ebi.ac.uk/pdbsum/4wqu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wqu ProSAT]</span></td></tr>
 </table>
@@ Line 21: / Line 22: @@
 ==See Also==
 *[[Elongation factor 3D structures|Elongation factor 3D structures]]
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
 *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
 == References ==

4wqu

From Proteopedia

Current revision

Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation factor G trapped by the antibiotic dityromycin

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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