3j3w

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'''Unreleased structure'''
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{{STRUCTURE_3j3w| PDB=3j3w | SCENE= }}
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===Atomic model of the immature 50S subunit from Bacillus subtilis (state II-a)===
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{{ABSTRACT_PUBMED_23700310}}
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The entry 3j3w is ON HOLD
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==Function==
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[[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/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/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/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/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/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/RL21_BACSU RL21_BACSU]] This protein binds to 23S rRNA in the presence of protein L20 (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/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/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/RL15_BACSU RL15_BACSU]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RL11_BACSU RL11_BACSU]] This protein binds directly to 23S ribosomal RNA (By similarity). [[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/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).
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Authors: Li, N, Guo, Q, Zhang, Y, Yuan, Y, Ma, C, Lei, J, Gao, N
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==About this Structure==
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[[3j3w]] is a 19 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=3J3W OCA].
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Description: Atomic model of the immature 50S subunit from Bacillus subtilis (state II-a)
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==Reference==
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<ref group="xtra">PMID:023700310</ref><references group="xtra"/><references/>
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[[Category: Bacillus subtilis]]
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[[Category: Gao, N.]]
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[[Category: Guo, Q.]]
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[[Category: Lei, J.]]
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[[Category: Li, N.]]
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[[Category: Ma, C.]]
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[[Category: Yuan, Y.]]
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[[Category: Zhang, Y.]]
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[[Category: Ribosome]]
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[[Category: Ribosome assembly]]
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[[Category: Ribosome biogenesis]]
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[[Category: Rna folding]]
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[[Category: Ylqf]]

Revision as of 15:27, 19 June 2013

Template:STRUCTURE 3j3w

Contents

Atomic model of the immature 50S subunit from Bacillus subtilis (state II-a)

Template:ABSTRACT PUBMED 23700310

Function

[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.[1] [RL14_BACSU] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome (By similarity). [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). [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). [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] [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] [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). [RL21_BACSU] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). [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). [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). [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).[2] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit (By similarity).[3] 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.[4] [RL15_BACSU] Binds to the 23S rRNA (By similarity). [RL11_BACSU] This protein binds directly to 23S ribosomal RNA (By similarity). [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). [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).

About this Structure

3j3w is a 19 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA.

Reference

  • Li N, Chen Y, Guo Q, Zhang Y, Yuan Y, Ma C, Deng H, Lei J, Gao N. Cryo-EM structures of the late-stage assembly intermediates of the bacterial 50S ribosomal subunit. Nucleic Acids Res. 2013 May 21. PMID:23700310 doi:10.1093/nar/gkt423
  1. ↑ Redko Y, Condon C. Ribosomal protein L3 bound to 23S precursor rRNA stimulates its maturation by Mini-III ribonuclease. Mol Microbiol. 2009 Mar;71(5):1145-54. doi: 10.1111/j.1365-2958.2008.06591.x., Epub 2009 Jan 16. PMID:19154332 doi:http://dx.doi.org/10.1111/j.1365-2958.2008.06591.x
  2. ↑ Exley R, Zouine M, Pernelle JJ, Beloin C, Le Hegarat F, Deneubourg AM. A possible role for L24 of Bacillus subtilis in nucleoid organization and segregation. Biochimie. 2001 Feb;83(2):269-75. PMID:11278078
  3. ↑ Exley R, Zouine M, Pernelle JJ, Beloin C, Le Hegarat F, Deneubourg AM. A possible role for L24 of Bacillus subtilis in nucleoid organization and segregation. Biochimie. 2001 Feb;83(2):269-75. PMID:11278078
  4. ↑ Exley R, Zouine M, Pernelle JJ, Beloin C, Le Hegarat F, Deneubourg AM. A possible role for L24 of Bacillus subtilis in nucleoid organization and segregation. Biochimie. 2001 Feb;83(2):269-75. PMID:11278078

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