4bye - Revision history

OCA: Redirecting to 4v8x

2014-12-10T15:41:04Z

Redirecting to 4v8x

← Older revision		Revision as of 15:41, 10 December 2014
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	~~{{Large structure}}~~		#REDIRECT [[4v8x]] This PDB entry is obsolete and replaced by 4v8x
	~~{{STRUCTURE_4bye\| PDB=4bye \| SCENE= }}~~
	~~===Structure of Thermus thermophilus 50S ribosome===~~
	~~{{ABSTRACT_PUBMED_23945936}}~~

	~~==Function==~~
	[[http://www.uniprot.org/uniprot/RL25_THET8 RL25_THET8]] This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit.[HAMAP-Rule:MF_01334] [[http://www.uniprot.org/uniprot/RL24_THET8 RL24_THET8]] 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).[HAMAP-Rule:MF_01326_B] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_B] [[http://www.uniprot.org/uniprot/RL13_THET8 RL13_THET8]] 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/RL33_THET8 RL33_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00294] Contacts the E site tRNA.[HAMAP-Rule:MF_00294] [[http://www.uniprot.org/uniprot/RL18_THET8 RL18_THET8]] This is ~~one of the proteins that binds~~ and mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.[HAMAP-Rule:MF_01337_B] [[http://www.uniprot.org/uniprot/RL5_THET8 RL5_THET8]] 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 (forming bridge B1b) connecting the head of the 30S subunit to the top of the 50S subunit. The bridge itself contacts the P site tRNA and is implicated in movement during ribosome translocation. Also contacts the P site tRNA independently of the intersubunit bridge; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://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] [[http://www.uniprot.org/uniprot/RL27_THET8 RL27_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00539] [[http://www.uniprot.org/uniprot/RL6_THET8 RL6_THET8]] 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.[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL22_THET8 RL22_THET8]] 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).[HAMAP-Rule:MF_01331_B] 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.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RL15_THET8 RL15_THET8]] Binds to the 23S rRNA (By similarity).[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RL1_THET8 RL1_THET8]] Directly binds to 23S rRNA. Forms what is known as the L1 stalk, which protrudes beyond the 70S ribosome surface. The stalk is preferentially stabilized in 70S versus 50S crystals. Interacts with the E site tRNA, blocking the exit path. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_01318_B] Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (By similarity).[HAMAP-Rule:MF_01318_B] [[http://www.uniprot.org/uniprot/RL4_THET8 RL4_THET8]] 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).[HAMAP-Rule:MF_01328_B] Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328_B] This protein can be incorporated into E.coli ribosomes in vivo, which resulted in decreased peptidyltransferase (Ptase) activity of the hybrid ribosomes. The hybrid 50S subunits associate less well with 30S subunits to form the ribosome.[HAMAP-Rule:MF_01328_B] [[http://www.uniprot.org/uniprot/RL21_THET8 RL21_THET8]] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). Found on the solvent side of the large subunit.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL32_THET8 RL32_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00340] [[http://www.uniprot.org/uniprot/RL19_THET8 RL19_THET8]] Contacts the 16S rRNA of the 30S subunit (part of bridge B6), connecting the 2 subunits.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RL20_THET8 RL20_THET8]] 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).[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RL29_THET8 RL29_THET8]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://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] [[http://www.uniprot.org/uniprot/RL3_THET8 RL3_THET8]] 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).[HAMAP-Rule:MF_01325_B] [[http://www.uniprot.org/uniprot/RL34_THET8 RL34_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00391] [[http://www.uniprot.org/uniprot/RL16_THET8 RL16_THET8]] This protein binds directly to 23S rRNA. Interacts with the A site tRNA.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL9_THET8 RL9_THET8]] Binds to the 23S rRNA. Extends more that 50 Angstroms beyond the surface of the 70S ribosome.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL23_THET8 RL23_THET8]] One of the early assembly proteins (By similarity) 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).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL31_THET8 RL31_THET8]] Binds the 23S rRNA (By similarity).[HAMAP-Rule:MF_00501]

	~~==About this Structure==~~
	[[4bye]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BYE OCA].

	~~==See Also==~~
	*[[Ribosomal protein L10\|Ribosomal protein L10]]
	*[[Ribosomal protein L13\|Ribosomal protein L13]]
	*[[Ribosomal protein L14\|Ribosomal protein L14]]
	*[[Ribosomal protein L15\|Ribosomal protein L15]]
	*[[Ribosomal protein L16\|Ribosomal protein L16]]
	*[[Ribosomal protein L17\|Ribosomal protein L17]]
	*[[Ribosomal protein L18\|Ribosomal protein L18]]
	*[[Ribosomal protein L19\|Ribosomal protein L19]]
	*[[Ribosomal protein L20\|Ribosomal protein L20]]
	*[[Ribosomal protein L21\|Ribosomal protein L21]]
	*[[Ribosomal protein L22\|Ribosomal protein L22]]
	*[[Ribosomal protein L23\|Ribosomal protein L23]]
	*[[Ribosomal protein L24\|Ribosomal protein L24]]
	*[[Ribosomal protein L25\|Ribosomal protein L25]]
	*[[Ribosomal protein L27\|Ribosomal protein L27]]
	*[[Ribosomal protein L28\|Ribosomal protein L28]]
	*[[Ribosomal protein L29\|Ribosomal protein L29]]
	*[[Ribosomal protein L30\|Ribosomal protein L30]]
	*[[Ribosomal protein L31\|Ribosomal protein L31]]
	*[[Ribosomal protein L32\|Ribosomal protein L32]]
	*[[Ribosomal protein L33\|Ribosomal protein L33]]
	*[[Ribosomal protein L34\|Ribosomal protein L34]]
	*[[Ribosomal protein L35\|Ribosomal protein L35]]
	*[[Ribosomal protein L36\|Ribosomal protein L36]]

	~~==Reference==~~
	~~<ref group="xtra">PMID:023945936</ref><references group="xtra"/><references/>~~
	~~[[Category: Thermus thermophilus]]~~
	~~[[Category: Chen, Y.]]~~
	~~[[Category: Feng, S.]]~~
	~~[[Category: Gao, Y G.]]~~
	~~[[Category: Kamada, K.]]~~
	~~[[Category: Tang, K.]]~~
	~~[[Category: Wang, H.]]~~
	~~[[Category: Wang, M.]]~~
	~~[[Category: Mrna degradation]]~~
	~~[[Category: Ribosome]]~~
	~~[[Category: Ribosome-dependent nuclease]]~~
	~~[[Category: Toxin-antitoxin]]~~
	~~[[Category: Translation regulation]]~~

OCA at 08:45, 25 December 2013

2013-12-25T08:45:07Z

@@ Line 20: / Line 20: @@
 *[[Ribosomal protein L19|Ribosomal protein L19]]
 *[[Ribosomal protein L20|Ribosomal protein L20]]
 ==Reference==

OCA at 06:32, 13 November 2013

2013-11-13T06:32:08Z

@@ Line 9: / Line 9: @@
 ==About this Structure==
 [[4bye]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4BYE OCA].
 ==Reference==

OCA at 07:29, 28 August 2013

2013-08-28T07:29:20Z

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-'''Unreleased structure'''
+{{Large structure}}
-The entry 4bye is ON HOLD
+==Function==
-Authors: Feng, S., Chen, Y., Kamada, K., Wang, H., Tang, K., Wang, M., Gao, Y.G.
+==About this Structure==
-Description: Structure of Thermus thermophilus 50S ribosome
+==Reference==

OCA: Protected "4bye" [edit=sysop:move=sysop]

2013-08-01T03:59:50Z

Protected "4bye" [edit=sysop:move=sysop]

← Older revision	Revision as of 03:59, 1 August 2013
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4bye is ON HOLD Authors: Feng, S., Chen, Y., Kamada, K., Wang, H., Tang, K., Wang, M., Gao, Y.G. Description: Structure of Thermus thermophilus 50S...

2013-08-01T03:59:49Z

New page: '''Unreleased structure''' The entry 4bye is ON HOLD Authors: Feng, S., Chen, Y., Kamada, K., Wang, H., Tang, K., Wang, M., Gao, Y.G. Description: Structure of Thermus thermophilus 50S...

New page

'''Unreleased structure'''

The entry 4bye is ON HOLD

Authors: Feng, S., Chen, Y., Kamada, K., Wang, H., Tang, K., Wang, M., Gao, Y.G.

Description: Structure of Thermus thermophilus 50S ribosome