5zep - Revision history

OCA at 22:52, 10 April 2020

OCA — Fri, 10 Apr 2020 22:52:31 GMT

←Older revision		Revision as of 22:52, 10 April 2020
Line 3:		Line 3:
	<SX load='5zep' size='340' side='right' viewer='molstar' caption='[[5zep]], [[Resolution\|resolution]] 3.40Å' scene=''>		<SX load='5zep' size='340' side='right' viewer='molstar' caption='[[5zep]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zep]] is a 57 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEP OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZEP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zep]] is a 57 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEP OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZEP FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</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=5zep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zep OCA], [http://pdbe.org/5zep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zep RCSB], [http://www.ebi.ac.uk/pdbsum/5zep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zep ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zep OCA], [http://pdbe.org/5zep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zep RCSB], [http://www.ebi.ac.uk/pdbsum/5zep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zep ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 20:17, 6 March 2020

OCA — Fri, 06 Mar 2020 20:17:57 GMT

←Older revision		Revision as of 20:17, 6 March 2020
Line 1:		Line 1:
-	~~{{Large structure}}~~	+
	==M. smegmatis hibernating state 70S ribosome structure==		==M. smegmatis hibernating state 70S ribosome structure==
-	<~~StructureSection~~ load='5zep' size='340' side='right' caption='[[5zep]], [[Resolution\|resolution]] 3.40Å' scene=''>	+	<SX load='5zep' size='340' side='right' viewer='molstar' caption='[[5zep]], [[Resolution\|resolution]] 3.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5zep]] is a 57 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZEP FirstGlance]. <br>		<table><tr><td colspan='2'>[[5zep]] is a 57 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZEP FirstGlance]. <br>
Line 7:		Line 7:
	<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=5zep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zep OCA], [http://pdbe.org/5zep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zep RCSB], [http://www.ebi.ac.uk/pdbsum/5zep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zep ProSAT]</span></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=5zep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zep OCA], [http://pdbe.org/5zep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zep RCSB], [http://www.ebi.ac.uk/pdbsum/5zep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zep ProSAT]</span></td></tr>
	</table>		</table>
-	{{Large structure}}
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RL13_MYCS2 RL13_MYCS2]] 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.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL11_MYCS2 RL11_MYCS2]] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.[HAMAP-Rule:MF_00736] [[http://www.uniprot.org/uniprot/RS10_MYCS2 RS10_MYCS2]] Involved in the binding of tRNA to the ribosomes. [[http://www.uniprot.org/uniprot/RL3_MYCS2 RL3_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS4_MYCS2 RS4_MYCS2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy~~. [[http://www.uniprot.org/uniprot/RS3_MYCS2 RS3_MYCS2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation~~. [[http://www.uniprot.org/uniprot/A0A0D6J3X3_MYCSM A0A0D6J3X3_MYCSM]] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360][SAAS:SAAS00348112] [[http://www.uniprot.org/uniprot/RL9_MYCS2 RL9_MYCS2]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RL24_MYCS2 RL24_MYCS2]] 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. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RL4_MYCS2 RL4_MYCS2]] 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.[HAMAP-Rule:MF_01328] Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/RL2_MYCS2 RL2_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL5_MYCS2 RL5_MYCS2]] 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.[HAMAP-Rule:MF_01333] [[http://www.uniprot.org/uniprot/RL20_MYCS2 RL20_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS20_MYCS2 RS20_MYCS2]] Binds directly to 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS15_MYCS2 RS15_MYCS2]] 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.[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RL10_MYCS2 RL10_MYCS2]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. [[http://www.uniprot.org/uniprot/A0QSG8_MYCS2 A0QSG8_MYCS2]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00687840] [[http://www.uniprot.org/uniprot/RS17_MYCS2 RS17_MYCS2]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL22_MYCS2 RL22_MYCS2]] 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] 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.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RS19_MYCS2 RS19_MYCS2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/A0QTK6_MYCS2 A0QTK6_MYCS2]] Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase; 100S ribosomes are translationally inactive and sometimes present during exponential growth.[HAMAP-Rule:MF_00839] [[http://www.uniprot.org/uniprot/RL6_MYCS2 RL6_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL31_MYCS2 RL31_MYCS2]] Binds the 23S rRNA. [[http://www.uniprot.org/uniprot/RL19_MYCS2 RL19_MYCS2]] 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~~. [[http://www.uniprot.org/uniprot/RL16_MYCS2 RL16_MYCS2]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs~~. [[http://www.uniprot.org/uniprot/RS5_MYCS2 RS5_MYCS2]] With S4 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01307] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.[HAMAP-Rule:MF_01307] [[http://www.uniprot.org/uniprot/RS12_MYCS2 RS12_MYCS2]] With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RL21_MYCS2 RL21_MYCS2]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RS182_MYCS2 RS182_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS14Z_MYCS2 RS14Z_MYCS2]] 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. [[http://www.uniprot.org/uniprot/I7FGD9_MYCS2 I7FGD9_MYCS2]] 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/RS11_MYCS2 RS11_MYCS2]] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. [[http://www.uniprot.org/uniprot/RS7_MYCS2 RS7_MYCS2]] One of the primary rRNA binding proteins, it binds directly to 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, probably blocks exit of the E-site tRNA. [[http://www.uniprot.org/uniprot/RL14_MYCS2 RL14_MYCS2]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [[http://www.uniprot.org/uniprot/I7GFB2_MYCS2 I7GFB2_MYCS2]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01334][SAAS:SAAS00720025] [[http://www.uniprot.org/uniprot/RL23_MYCS2 RL23_MYCS2]] 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.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RS13_MYCS2 RS13_MYCS2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. [[http://www.uniprot.org/uniprot/RS8_MYCS2 RS8_MYCS2]] 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.[HAMAP-Rule:MF_01302]	+	[[http://www.uniprot.org/uniprot/RL13_MYCS2 RL13_MYCS2]] 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.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL11_MYCS2 RL11_MYCS2]] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.[HAMAP-Rule:MF_00736] [[http://www.uniprot.org/uniprot/RS10_MYCS2 RS10_MYCS2]] Involved in the binding of tRNA to the ribosomes. [[http://www.uniprot.org/uniprot/RL3_MYCS2 RL3_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS3_MYCS2 RS3_MYCS2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. [[http://www.uniprot.org/uniprot/RS4_MYCS2 RS4_MYCS2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. [[http://www.uniprot.org/uniprot/A0A0D6J3X3_MYCSM A0A0D6J3X3_MYCSM]] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360][SAAS:SAAS00348112] [[http://www.uniprot.org/uniprot/RL9_MYCS2 RL9_MYCS2]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RL24_MYCS2 RL24_MYCS2]] 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. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RL4_MYCS2 RL4_MYCS2]] 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.[HAMAP-Rule:MF_01328] Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/RL2_MYCS2 RL2_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL5_MYCS2 RL5_MYCS2]] 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.[HAMAP-Rule:MF_01333] [[http://www.uniprot.org/uniprot/RL20_MYCS2 RL20_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS20_MYCS2 RS20_MYCS2]] Binds directly to 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS15_MYCS2 RS15_MYCS2]] 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.[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RL10_MYCS2 RL10_MYCS2]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. [[http://www.uniprot.org/uniprot/A0QSG8_MYCS2 A0QSG8_MYCS2]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00687840] [[http://www.uniprot.org/uniprot/RS17_MYCS2 RS17_MYCS2]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL22_MYCS2 RL22_MYCS2]] 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] 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.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RS19_MYCS2 RS19_MYCS2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/A0QTK6_MYCS2 A0QTK6_MYCS2]] Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase; 100S ribosomes are translationally inactive and sometimes present during exponential growth.[HAMAP-Rule:MF_00839] [[http://www.uniprot.org/uniprot/RL6_MYCS2 RL6_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL31_MYCS2 RL31_MYCS2]] Binds the 23S rRNA. [[http://www.uniprot.org/uniprot/RL19_MYCS2 RL19_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS5_MYCS2 RS5_MYCS2]] With S4 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01307] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.[HAMAP-Rule:MF_01307] [[http://www.uniprot.org/uniprot/RL16_MYCS2 RL16_MYCS2]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [[http://www.uniprot.org/uniprot/RS12_MYCS2 RS12_MYCS2]] With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RL21_MYCS2 RL21_MYCS2]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RS182_MYCS2 RS182_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS14Z_MYCS2 RS14Z_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS11_MYCS2 RS11_MYCS2]] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. [[http://www.uniprot.org/uniprot/I7FGD9_MYCS2 I7FGD9_MYCS2]] 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/RS7_MYCS2 RS7_MYCS2]] One of the primary rRNA binding proteins, it binds directly to 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, probably blocks exit of the E-site tRNA. [[http://www.uniprot.org/uniprot/RL14_MYCS2 RL14_MYCS2]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [[http://www.uniprot.org/uniprot/I7GFB2_MYCS2 I7GFB2_MYCS2]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01334][SAAS:SAAS00720025] [[http://www.uniprot.org/uniprot/RL23_MYCS2 RL23_MYCS2]] 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.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RS13_MYCS2 RS13_MYCS2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. [[http://www.uniprot.org/uniprot/RS8_MYCS2 RS8_MYCS2]] 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.[HAMAP-Rule:MF_01302]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5zep" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5zep" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
		+	[[Category: Large Structures]]
	[[Category: Mycobacterium smegmatis str. mc2 155]]		[[Category: Mycobacterium smegmatis str. mc2 155]]
	[[Category: Ahmed, T]]		[[Category: Ahmed, T]]

OCA at 07:56, 26 September 2018

OCA — Wed, 26 Sep 2018 07:56:14 GMT

←Older revision		Revision as of 07:56, 26 September 2018
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-	'''~~Unreleased~~ structure'''	+	{{Large structure}}
		+	==M. smegmatis hibernating state 70S ribosome structure==
		+	<StructureSection load='5zep' size='340' side='right' caption='[[5zep]], [[Resolution\|resolution]] 3.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zep]] is a 57 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Mycobacterium_smegmatis_str._mc2_155 Mycobacterium smegmatis str. mc2 155]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZEP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZEP FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</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=5zep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zep OCA], [http://pdbe.org/5zep PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zep RCSB], [http://www.ebi.ac.uk/pdbsum/5zep PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zep ProSAT]</span></td></tr>
		+	</table>
		+	{{Large structure}}
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RL13_MYCS2 RL13_MYCS2]] 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.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL11_MYCS2 RL11_MYCS2]] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.[HAMAP-Rule:MF_00736] [[http://www.uniprot.org/uniprot/RS10_MYCS2 RS10_MYCS2]] Involved in the binding of tRNA to the ribosomes. [[http://www.uniprot.org/uniprot/RL3_MYCS2 RL3_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS4_MYCS2 RS4_MYCS2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. [[http://www.uniprot.org/uniprot/RS3_MYCS2 RS3_MYCS2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. [[http://www.uniprot.org/uniprot/A0A0D6J3X3_MYCSM A0A0D6J3X3_MYCSM]] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360][SAAS:SAAS00348112] [[http://www.uniprot.org/uniprot/RL9_MYCS2 RL9_MYCS2]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RL24_MYCS2 RL24_MYCS2]] 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. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. [[http://www.uniprot.org/uniprot/RL4_MYCS2 RL4_MYCS2]] 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.[HAMAP-Rule:MF_01328] Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/RL2_MYCS2 RL2_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL5_MYCS2 RL5_MYCS2]] 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.[HAMAP-Rule:MF_01333] [[http://www.uniprot.org/uniprot/RL20_MYCS2 RL20_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS20_MYCS2 RS20_MYCS2]] Binds directly to 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS15_MYCS2 RS15_MYCS2]] 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.[HAMAP-Rule:MF_01343] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RL10_MYCS2 RL10_MYCS2]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. [[http://www.uniprot.org/uniprot/A0QSG8_MYCS2 A0QSG8_MYCS2]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00687840] [[http://www.uniprot.org/uniprot/RS17_MYCS2 RS17_MYCS2]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL22_MYCS2 RL22_MYCS2]] 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] 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.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RS19_MYCS2 RS19_MYCS2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/A0QTK6_MYCS2 A0QTK6_MYCS2]] Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase; 100S ribosomes are translationally inactive and sometimes present during exponential growth.[HAMAP-Rule:MF_00839] [[http://www.uniprot.org/uniprot/RL6_MYCS2 RL6_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL31_MYCS2 RL31_MYCS2]] Binds the 23S rRNA. [[http://www.uniprot.org/uniprot/RL19_MYCS2 RL19_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RL16_MYCS2 RL16_MYCS2]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [[http://www.uniprot.org/uniprot/RS5_MYCS2 RS5_MYCS2]] With S4 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01307] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body.[HAMAP-Rule:MF_01307] [[http://www.uniprot.org/uniprot/RS12_MYCS2 RS12_MYCS2]] With S4 and S5 plays an important role in translational accuracy. Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RL21_MYCS2 RL21_MYCS2]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RS182_MYCS2 RS182_MYCS2]] 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. [[http://www.uniprot.org/uniprot/RS14Z_MYCS2 RS14Z_MYCS2]] 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. [[http://www.uniprot.org/uniprot/I7FGD9_MYCS2 I7FGD9_MYCS2]] 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.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/RS11_MYCS2 RS11_MYCS2]] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. [[http://www.uniprot.org/uniprot/RS7_MYCS2 RS7_MYCS2]] One of the primary rRNA binding proteins, it binds directly to 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, probably blocks exit of the E-site tRNA. [[http://www.uniprot.org/uniprot/RL14_MYCS2 RL14_MYCS2]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [[http://www.uniprot.org/uniprot/I7GFB2_MYCS2 I7GFB2_MYCS2]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01334][SAAS:SAAS00720025] [[http://www.uniprot.org/uniprot/RL23_MYCS2 RL23_MYCS2]] 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.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RS13_MYCS2 RS13_MYCS2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites. [[http://www.uniprot.org/uniprot/RS8_MYCS2 RS8_MYCS2]] 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.[HAMAP-Rule:MF_01302]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand their mechanism of action. Here, we present single particle cryo-EM reconstructions of the Mycobacterium smegmatis 70S ribosomes in the hibernating state (with HPF), trans-translating state (with tmRNA), and the P/P state (with P-tRNA) resolved to 4.1, 12.5, and 3.4 A, respectively. A comparison of the P/P state with the hibernating state provides possible functional insights about the Mycobacteria-specific helix H54a rRNA segment. Interestingly, densities for all the four OB domains of bS1 protein is visible in the hibernating 70S ribosome displaying the molecular details of bS1-70S interactions. Our structural data shows a Mycobacteria-specific H54a-bS1 interaction which seems to prevent subunit dissociation and degradation during hibernation without the formation of 100S dimer. This indicates a new role of bS1 protein in 70S protection during hibernation in Mycobacteria in addition to its conserved function during translation initiation.

-	~~The entry 5zep is ON HOLD~~	+	Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA.,Mishra S, Ahmed T, Tyagi A, Shi J, Bhushan S Sci Rep. 2018 Sep 11;8(1):13587. doi: 10.1038/s41598-018-31850-3. PMID:30206241<ref>PMID:30206241</ref>

-	~~Authors: Mishra~~, S.~~, Ahmed, T., Tyagi, A., Shi, J., Bhushan, S~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~M. smegmatis hibernating state 70S ribosome structure~~	+	<div class="pdbe-citations 5zep" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: ~~Tyagi, A~~]]	+	<references/>
-	[[Category: ~~Shi~~, J]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia coli]]
		+	[[Category: Mycobacterium smegmatis str. mc2 155]]
		+	[[Category: Ahmed, T]]
	[[Category: Bhushan, S]]		[[Category: Bhushan, S]]
-	[[Category: Ahmed, T]]
	[[Category: Mishra, S]]		[[Category: Mishra, S]]
		+	[[Category: Shi, J]]
		+	[[Category: Tyagi, A]]
		+	[[Category: Complex]]
		+	[[Category: Hibernating-state]]
		+	[[Category: Ribosome]]

OCA at 03:52, 11 July 2018

OCA — Wed, 11 Jul 2018 03:52:16 GMT

←Older revision		Revision as of 03:52, 11 July 2018
Line 5:		Line 5:
	Authors: Mishra, S., Ahmed, T., Tyagi, A., Shi, J., Bhushan, S.		Authors: Mishra, S., Ahmed, T., Tyagi, A., Shi, J., Bhushan, S.

-	Description: ~~Structure of the~~ hibernating state 70S ribosome ~~from M. smegmatis~~	+	Description: M. smegmatis hibernating state 70S ribosome structure
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Ahmed, T]]
	[[Category: Tyagi, A]]		[[Category: Tyagi, A]]
	[[Category: Shi, J]]		[[Category: Shi, J]]
	[[Category: Bhushan, S]]		[[Category: Bhushan, S]]
		+	[[Category: Ahmed, T]]
	[[Category: Mishra, S]]		[[Category: Mishra, S]]

OCA: Protected "5zep" [edit=sysop:move=sysop]

OCA — Thu, 08 Mar 2018 03:39:19 GMT

Protected "5zep" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:39, 8 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zep is ON HOLD Authors: Mishra, S., Ahmed, T., Tyagi, A., Shi, J., Bhushan, S. Description: Structure of the hibernating state 70S ribosome from M...

OCA — Thu, 08 Mar 2018 03:39:18 GMT

New page: '''Unreleased structure''' The entry 5zep is ON HOLD Authors: Mishra, S., Ahmed, T., Tyagi, A., Shi, J., Bhushan, S. Description: Structure of the hibernating state 70S ribosome from M...

New page

'''Unreleased structure'''

The entry 5zep is ON HOLD

Authors: Mishra, S., Ahmed, T., Tyagi, A., Shi, J., Bhushan, S.

Description: Structure of the hibernating state 70S ribosome from M. smegmatis
[[Category: Unreleased Structures]]
[[Category: Ahmed, T]]
[[Category: Tyagi, A]]
[[Category: Shi, J]]
[[Category: Bhushan, S]]
[[Category: Mishra, S]]