8bh4

From Proteopedia

(Difference between revisions)

Current revision

Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAm6A mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site

Structural highlights

8bh4 is a 10 chain structure with sequence from Escherichia coli K-12 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.62Å
Ligands:	, , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RL2_ECOLI One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. 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 highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B]

Publication Abstract from PubMed

N(6)-methyladenosine (m(6)A) is an abundant, dynamic mRNA modification that regulates key steps of cellular mRNA metabolism. m(6)A in the mRNA coding regions inhibits translation elongation. Here, we show how m(6)A modulates decoding in the bacterial translation system using a combination of rapid kinetics, smFRET and single-particle cryo-EM. We show that, while the modification does not impair the initial binding of aminoacyl-tRNA to the ribosome, in the presence of m(6)A fewer ribosomes complete the decoding process due to the lower stability of the complexes and enhanced tRNA drop-off. The mRNA codon adopts a pi-stacked codon conformation that is remodeled upon aminoacyl-tRNA binding. m(6)A does not exclude canonical codon-anticodon geometry, but favors alternative more dynamic conformations that are rejected by the ribosome. These results highlight how modifications outside the Watson-Crick edge can still interfere with codon-anticodon base pairing and complex recognition by the ribosome, thereby modulating the translational efficiency of modified mRNAs.

Modulation of translational decoding by m(6)A modification of mRNA.,Jain S, Koziej L, Poulis P, Kaczmarczyk I, Gaik M, Rawski M, Ranjan N, Glatt S, Rodnina MV Nat Commun. 2023 Aug 8;14(1):4784. doi: 10.1038/s41467-023-40422-7. PMID:37553384^[1]

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

References

↑ Jain S, Koziej L, Poulis P, Kaczmarczyk I, Gaik M, Rawski M, Ranjan N, Glatt S, Rodnina MV. Modulation of translational decoding by m(6)A modification of mRNA. Nat Commun. 2023 Aug 8;14(1):4784. PMID:37553384 doi:10.1038/s41467-023-40422-7

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/8bh4"

Categories: Escherichia coli K-12 | Large Structures | Synthetic construct | Glatt S | Koziej L

@@ Line 3: / Line 3: @@
 <StructureSection load='8bh4' size='340' side='right'caption='[[8bh4]], [[Resolution|resolution]] 2.62&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[8bh4]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BH4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[8bh4]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8BH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8BH4 FirstGlance]. <br>
 </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.62&#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=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=T6A:N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)CARBAMOYL]THREONINE-5-MONOPHOSPHATE'>T6A</scene>, <scene name='pdbligand=U8U:5-METHYLAMINOMETHYL-2-THIOURIDINE-5-MONOPHOSPHATE'>U8U</scene></td></tr>
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 8bh4" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribosome 3D structures|Ribosome 3D structures]]
 == References ==
 <references/>
@@ Line 25: / Line 28: @@
 [[Category: Escherichia coli K-12]]
 [[Category: Large Structures]]
+[[Category: Synthetic construct]]
 [[Category: Glatt S]]
 [[Category: Koziej L]]

8bh4

From Proteopedia

Current revision

Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAm6A mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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