4v4t: Difference between revisions

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New page: ==Crystal structure of the whole ribosomal complex with a stop codon in the A-site.== <StructureSection load='4v4t' size='340' side='right' caption='4v4t, resolution 6.4...
 
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==Crystal structure of the whole ribosomal complex with a stop codon in the A-site.==
==Crystal structure of the whole ribosomal complex with a stop codon in the A-site.==
<StructureSection load='4v4t' size='340' side='right' caption='[[4v4t]], [[Resolution|resolution]] 6.46&Aring;' scene=''>
<StructureSection load='4v4t' size='340' side='right'caption='[[4v4t]], [[Resolution|resolution]] 6.46&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4v4t]] is a 55 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes the now removed PDB entries and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2b9p 2b9p]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V4T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V4T FirstGlance]. <br>
<table><tr><td colspan='2'>[[4v4t]] is a 10 chain structure with sequence from [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=2b9o 2b9o] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2b9p 2b9p]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V4T FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YYG:4-(3-[5-O-PHOSPHONORIBOFURANOSYL]-4,6-DIMETHYL-8-OXO-4,8-DIHYDRO-3H-1,3,4,5,7A-PENTAAZA-S-INDACEN-YLAMINO-BUTYRIC+ACID+METHYL+ESTER'>YYG</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]] 6.46&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2b9o|2b9o]], [[2b9p|2b9p]], [[2b64|2b64]], [[2b66|2b66]], [[2b9m|2b9m]], [[2b9n|2b9n]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=YYG:4-(3-[5-O-PHOSPHONORIBOFURANOSYL]-4,6-DIMETHYL-8-OXO-4,8-DIHYDRO-3H-1,3,4,5,7A-PENTAAZA-S-INDACEN-YLAMINO-BUTYRIC+ACID+METHYL+ESTER'>YYG</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4v4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v4t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4v4t RCSB], [http://www.ebi.ac.uk/pdbsum/4v4t PDBsum]</span></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=4v4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v4t OCA], [https://pdbe.org/4v4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v4t RCSB], [https://www.ebi.ac.uk/pdbsum/4v4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v4t ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/RS18_THETH RS18_THETH]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS14Z_THETH RS14Z_THETH]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS15_THETH RS15_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA.  Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RS17_THETH RS17_THETH]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THETH RSHX_THETH]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS8_THETH RS8_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS19_THETH RS19_THETH]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS10_THETH RS10_THETH]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RL22_THETH RL22_THETH]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).  The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome. This extension seems to form part of the wall of the exit tunnel (By similarity). Deleting residues 82 to 84 (the equivalent deletion in E.coli renders cells resistant to erythromycin) would probably cause the tip of the hairpin to penetrate into the tunnel. [[http://www.uniprot.org/uniprot/RS6_THETH RS6_THETH]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS5_THETH RS5_THETH]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B]  Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).[HAMAP-Rule:MF_01307_B] [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]  
[https://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B]
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
<div class="pdbe-citations 4v4t" style="background-color:#fffaf0;"></div>
==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 ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Thermus thermophilus]]
[[Category: Large Structures]]
[[Category: Brodersen, D E]]
[[Category: Thermus thermophilus HB8]]
[[Category: Dunham, C M]]
[[Category: Brodersen DE]]
[[Category: IV, F V.Murphy]]
[[Category: Dunham CM]]
[[Category: Kelley, A C]]
[[Category: Kelley AC]]
[[Category: Petry, S]]
[[Category: Murphy IV FV]]
[[Category: Ramakrishnan, V]]
[[Category: Petry S]]
[[Category: Selmer, M]]
[[Category: Ramakrishnan V]]
[[Category: Tarry, M J]]
[[Category: Selmer M]]
[[Category: Ribosome]]
[[Category: Tarry MJ]]
[[Category: Translation]]

Latest revision as of 21:03, 20 September 2023

Crystal structure of the whole ribosomal complex with a stop codon in the A-site.Crystal structure of the whole ribosomal complex with a stop codon in the A-site.

Structural highlights

4v4t is a 10 chain structure with sequence from Thermus thermophilus HB8. This structure supersedes the now removed PDB entries 2b9o and 2b9p. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 6.46Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RS3_THET8 Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B]

Publication Abstract from PubMed

During protein synthesis, translational release factors catalyze the release of the polypeptide chain when a stop codon on the mRNA reaches the A site of the ribosome. The detailed mechanism of this process is currently unknown. We present here the crystal structures of the ribosome from Thermus thermophilus with RF1 and RF2 bound to their cognate stop codons, at resolutions of 5.9 Angstrom and 6.7 Angstrom, respectively. The structures reveal details of interactions of the factors with the ribosome and mRNA, including elements previously implicated in decoding and peptide release. They also shed light on conformational changes both in the factors and in the ribosome during termination. Differences seen in the interaction of RF1 and RF2 with the L11 region of the ribosome allow us to rationalize previous biochemical data. Finally, this work demonstrates the feasibility of crystallizing ribosomes with bound factors at a defined state along the translational pathway.

Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon.,Petry S, Brodersen DE, Murphy FV 4th, Dunham CM, Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V Cell. 2005 Dec 29;123(7):1255-66. PMID:16377566[1]

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

See Also

References

  1. ↑ Petry S, Brodersen DE, Murphy FV 4th, Dunham CM, Selmer M, Tarry MJ, Kelley AC, Ramakrishnan V. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell. 2005 Dec 29;123(7):1255-66. PMID:16377566 doi:http://dx.doi.org/10.1016/j.cell.2005.09.039

4v4t, resolution 6.46Å

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