4w2e: Difference between revisions

Latest revision as of 11:54, 13 August 2026

Crystal structure of Elongation Factor 4 (EF4/LepA) bound to the Thermus thermophilus 70S ribosome

Structural highlights

4w2e 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 2.9Å
Ligands:	4SU, 5MU, 7MG, GDP, MG, MIA, PHE, PSU, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL14_THET8 This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_01367] Contacts the 16S rRNA of the 30S subunit in two different positions helping to form bridges B5 and B8.[HAMAP-Rule:MF_01367]

Publication Abstract from PubMed

Elongation factor 4 (EF4/LepA) is a highly conserved guanosine triphosphatase translation factor. It was shown to promote back-translocation of tRNAs on posttranslocational ribosome complexes and to compete with elongation factor G for interaction with pretranslocational ribosomes, inhibiting the elongation phase of protein synthesis. Here, we report a crystal structure of EF4-guanosine diphosphate bound to the Thermus thermophilus ribosome with a P-site tRNA at 2.9 angstroms resolution. The C-terminal domain of EF4 reaches into the peptidyl transferase center and interacts with the acceptor stem of the peptidyl-tRNA in the P site. The ribosome is in an unusual state of ratcheting with the 30S subunit rotated clockwise relative to the 50S subunit, resulting in a remodeled decoding center. The structure is consistent with EF4 functioning either as a back-translocase or a ribosome sequester.

Ribosome structure. Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome.,Gagnon MG, Lin J, Bulkley D, Steitz TA Science. 2014 Aug 8;345(6197):684-7. doi: 10.1126/science.1253525. PMID:25104389^[1]

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

References

↑ Gagnon MG, Lin J, Bulkley D, Steitz TA. Ribosome structure. Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome. Science. 2014 Aug 8;345(6197):684-7. doi: 10.1126/science.1253525. PMID:25104389 doi:https://dx.doi.org/10.1126/science.1253525

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OCA

[1] Gagnon MG, Lin J, Bulkley D, Steitz TA. Ribosome structure. Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome. Science. 2014 Aug 8;345(6197):684-7. doi: 10.1126/science.1253525. PMID:25104389 doi:https://dx.doi.org/10.1126/science.1253525

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='4w2e' size='340' side='right'caption='[[4w2e]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4w2e]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] and [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qjs 4qjs] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qjt 4qjt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W2E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4w2e]] 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=4W2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W2E 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]] 2.9&#8491;</td></tr>
-<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=F3O:3-O-L-PHENYLALANYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>F3O</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=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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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=4w2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w2e OCA], [https://pdbe.org/4w2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w2e RCSB], [https://www.ebi.ac.uk/pdbsum/4w2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w2e ProSAT]</span></td></tr>
 </table>
 == Function ==
-[https://www.uniprot.org/uniprot/RL2_THET8 RL2_THET8] 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 (By similarity). Makes several contacts with the 16S rRNA (forming bridge B7b) in the 70S ribosome.[HAMAP-Rule:MF_01320_B]
+[https://www.uniprot.org/uniprot/RL14_THET8 RL14_THET8] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_01367]  Contacts the 16S rRNA of the 30S subunit in two different positions helping to form bridges B5 and B8.[HAMAP-Rule:MF_01367]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / 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 ==
@@ Line 28: / Line 30: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Thermus thermophilus]]
 [[Category: Thermus thermophilus HB8]]
 [[Category: Gagnon MG]]
 [[Category: Lin J]]
 [[Category: Steitz TA]]

4w2e: Difference between revisions

Latest revision as of 11:54, 13 August 2026

Crystal structure of Elongation Factor 4 (EF4/LepA) bound to the Thermus thermophilus 70S ribosome

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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