View source for 3j3v


==Atomic model of the immature 50S subunit from Bacillus subtilis (state I-a)==
<SX load='3j3v' size='340' side='right' viewer='molstar' caption='[[3j3v]], [[Resolution|resolution]] 13.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3j3v]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3J3V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3J3V FirstGlance]. <br>
</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3j3w|3j3w]]</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=3j3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3j3v OCA], [http://pdbe.org/3j3v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3j3v RCSB], [http://www.ebi.ac.uk/pdbsum/3j3v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3j3v ProSAT]</span></td></tr>
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== Function ==
[[http://www.uniprot.org/uniprot/RL6_BACSU RL6_BACSU]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center (By similarity). [[http://www.uniprot.org/uniprot/RL23_BACSU RL23_BACSU]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RL2_BACSU RL2_BACSU]] 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] [[http://www.uniprot.org/uniprot/RL19_BACSU RL19_BACSU]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site (By similarity). [[http://www.uniprot.org/uniprot/RL24_BACSU RL24_BACSU]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).<ref>PMID:11278078</ref>   One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).<ref>PMID:11278078</ref>   Has also been isolated as a basic, heat-shock stable DNA-binding protein from the B.subtilis nucleoid. It binds cooperatively to double-stranded supercoiled DNA which it further compacts into complexes 15-17 nm in diameter. Overexpression of the protein disrupts nucleoid segregation and positioning.<ref>PMID:11278078</ref>  [[http://www.uniprot.org/uniprot/RL20_BACSU RL20_BACSU]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity). [[http://www.uniprot.org/uniprot/RL14_BACSU RL14_BACSU]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RL18_BACSU RL18_BACSU]] This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance (By similarity).<ref>PMID:6432797</ref>   Required for correct processing of both the 5' and 3' ends of 5S rRNA precursor, which is does in conjunction with ribonuclease M5 (RNase M5, rnmV). Possibly folds the 5S rRNA precursor into the correct conformation, thus acting as a chaperone.<ref>PMID:6432797</ref>  [[http://www.uniprot.org/uniprot/RL1_BACSU RL1_BACSU]] Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release (By similarity).  Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (By similarity). [[http://www.uniprot.org/uniprot/RL4_BACSU RL4_BACSU]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. 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).  Forms part of the polypeptide exit tunnel (By similarity). [[http://www.uniprot.org/uniprot/RL13_BACSU RL13_BACSU]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL15_BACSU RL15_BACSU]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RL22_BACSU RL22_BACSU]] 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 located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RL3_BACSU RL3_BACSU]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity). Strongly stimulates 23S rRNA precursor processing by mini-ribonuclease 3 (MrnC); 20-30% DMSO can replace L3, suggesting the protein may alter rRNA conformation.<ref>PMID:19154332</ref>  [[http://www.uniprot.org/uniprot/RL11_BACSU RL11_BACSU]] This protein binds directly to 23S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RL5_BACSU RL5_BACSU]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs (By similarity). [[http://www.uniprot.org/uniprot/RL21_BACSU RL21_BACSU]] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). 
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== Publication Abstract from PubMed ==
Ribosome assembly is a process fundamental for all cellular activities. The efficiency and accuracy of the subunit assembly are tightly regulated and closely monitored. In the present work, we characterized, both compositionally and structurally, a set of in vivo 50S subunit precursors (45S), isolated from a mutant bacterial strain. Our qualitative mass spectrometry data indicate that L28, L16, L33, L36 and L35 are dramatically underrepresented in the 45S particles. This protein spectrum shows interesting similarity to many qualitatively analyzed 50S precursors from different genetic background, indicating the presence of global rate-limiting steps in the late-stage assembly of 50S subunit. Our structural data reveal two major intermediate states for the 45S particles. Consistently, both states severally lack those proteins, but they also differ in the stability of the functional centers of the 50S subunit, demonstrating that they are translationally inactive. Detailed analysis indicates that the orientation of H38 accounts for the global conformational differences in these intermediate structures, and suggests that the reorientation of H38 to its native position is rate-limiting during the late-stage assembly. Especially, H38 plays an essential role in stabilizing the central protuberance, through the interaction with the 5S rRNA, and the correctly orientated H38 is likely a prerequisite for further maturation of the 50S subunit.

Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit.,Li N, Chen Y, Guo Q, Zhang Y, Yuan Y, Ma C, Deng H, Lei J, Gao N Nucleic Acids Res. 2013 May 21. PMID:23700310<ref>PMID:23700310</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 3j3v" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
<references/>
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</SX>
[[Category: Bacillus subtilis]]
[[Category: Large Structures]]
[[Category: Gao, N]]
[[Category: Guo, Q]]
[[Category: Lei, J]]
[[Category: Li, N]]
[[Category: Ma, C]]
[[Category: Yuan, Y]]
[[Category: Zhang, Y]]
[[Category: Ribosome]]
[[Category: Ribosome assembly]]
[[Category: Ribosome biogenesis]]
[[Category: Rna folding]]
[[Category: Ylqf]]