6nqb

From Proteopedia

(Difference between revisions)

Revision as of 03:29, 11 April 2020

Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit

6nqb, resolution 3.80Å

Structural highlights

6nqb is a 16 chain structure with sequence from [1], "bacillus_coli"_migula_1895 "bacillus coli" migula 1895 and Escherichia coli h736. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	rpsC, NCTC9094_00425 ("Bacillus coli" Migula 1895), rpsL, EC970259_3994 ("Bacillus coli" Migula 1895), rpsR, HMPREF9534_03906 ("Bacillus coli" Migula 1895), rpsT, G749_00187 ("Bacillus coli" Migula 1895), rpsB, HMPREF1620_04659 ("Bacillus coli" Migula 1895), rpsJ, HMPREF9552_00980 ("Bacillus coli" Migula 1895), rpsN, C0R28_24180, D9J44_12955, ERS085374_04715, SAMEA3485113_04711 ("Bacillus coli" Migula 1895), rpsS, ECHG_03182 (Escherichia coli H736), rpsD, A1UM_03988 ("Bacillus coli" Migula 1895), rpsE, AOX65_22485 ("Bacillus coli" Migula 1895), rpsF, B9M99_08080, BE963_12515, BMT53_12235, CIJ94_19015, D2188_21030, DTM45_20815, DU321_10545, Eco118UI_24760, ECONIH1_24970, EFV14_11625, EIA08_19855, HMPREF3040_03088, NCTC9077_05624 ("Bacillus coli" Migula 1895), rpsH, HMPREF9530_00381 ("Bacillus coli" Migula 1895)
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[L3PZ69_ECOLX] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.[HAMAP-Rule:MF_01306] With S5 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01306] [RS15_ECO57] 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 (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [A0A090BZT4_ECOLX] 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.[HAMAP-Rule:MF_00537] [RS5_ECOK1] With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. [D8A1L7_ECOMS] 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] [D7X302_ECOLX] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508] [T6N332_ECOLX] Binds directly to 16S ribosomal RNA.[HAMAP-Rule:MF_00500] [D7ZI16_ECOLX] 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.[HAMAP-Rule:MF_00270] [A0A074QGH8_ECOLX] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360][SAAS:SAAS00348112] [F4SQ43_ECOLX] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.[HAMAP-Rule:MF_00531] [A0A376HTV6_ECOLX] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309] [V6FZ95_ECOLX] 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.[HAMAP-Rule:MF_00403][RuleBase:RU003623] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403][RuleBase:RU003623] [A0A0G3QJD8_9GAMM] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.[HAMAP-Rule:MF_01345]

Publication Abstract from PubMed

Assembly factors provide speed and directionality to the maturation process of the 30S subunit in bacteria. To gain a more precise understanding of how these proteins mediate 30S maturation, it is important to expand on studies of 30S assembly intermediates purified from bacterial strains lacking particular maturation factors. To reveal the role of the essential protein Era in the assembly of the 30S ribosomal subunit, we analyzed assembly intermediates that accumulated in Era-depleted Escherichia coli cells using quantitative mass spectrometry, high resolution cryo-electron microscopy and in-cell footprinting. Our combined approach allowed for visualization of the small subunit as it assembled and revealed that with the exception of key helices in the platform domain, all other 16S rRNA domains fold even in the absence of Era. Notably, the maturing particles did not stall while waiting for the platform domain to mature and instead re-routed their folding pathway to enable concerted maturation of other structural motifs spanning multiple rRNA domains. We also found that binding of Era to the mature 30S subunit destabilized helix 44 and the decoding center preventing binding of YjeQ, another assembly factor. This work establishes Era's role in ribosome assembly and suggests new roles in maintaining ribosome homeostasis.

Role of Era in assembly and homeostasis of the ribosomal small subunit.,Razi A, Davis JH, Hao Y, Jahagirdar D, Thurlow B, Basu K, Jain N, Gomez-Blanco J, Britton RA, Vargas J, Guarne A, Woodson SA, Williamson JR, Ortega J Nucleic Acids Res. 2019 Jul 2. pii: 5527280. doi: 10.1093/nar/gkz571. PMID:31265110^[1]

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

References

↑ Razi A, Davis JH, Hao Y, Jahagirdar D, Thurlow B, Basu K, Jain N, Gomez-Blanco J, Britton RA, Vargas J, Guarne A, Woodson SA, Williamson JR, Ortega J. Role of Era in assembly and homeostasis of the ribosomal small subunit. Nucleic Acids Res. 2019 Jul 2. pii: 5527280. doi: 10.1093/nar/gkz571. PMID:31265110 doi:http://dx.doi.org/10.1093/nar/gkz571

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6nqb"

@@ Line 3: / Line 3: @@
 <SX load='6nqb' size='340' side='right' viewer='molstar' caption='[[6nqb]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6nqb]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli_h736 Escherichia coli h736]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NQB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NQB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6nqb]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli_h736 Escherichia coli h736]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NQB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6NQB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rpsC, NCTC9094_00425 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpsL, EC970259_3994 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpsR, HMPREF9534_03906 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpsT, G749_00187 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpsB, HMPREF1620_04659 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpsJ, HMPREF9552_00980 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpsN, C0R28_24180, D9J44_12955, ERS085374_04715, SAMEA3485113_04711 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpsS, ECHG_03182 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=656414 Escherichia coli H736]), rpsD, A1UM_03988 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpsE, AOX65_22485 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpsF, B9M99_08080, BE963_12515, BMT53_12235, CIJ94_19015, D2188_21030, DTM45_20815, DU321_10545, Eco118UI_24760, ECONIH1_24970, EFV14_11625, EIA08_19855, HMPREF3040_03088, NCTC9077_05624 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895]), rpsH, HMPREF9530_00381 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=6nqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nqb OCA], [http://pdbe.org/6nqb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nqb RCSB], [http://www.ebi.ac.uk/pdbsum/6nqb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nqb 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=6nqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nqb OCA], [http://pdbe.org/6nqb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nqb RCSB], [http://www.ebi.ac.uk/pdbsum/6nqb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nqb ProSAT]</span></td></tr>
 </table>
 == Function ==

6nqb

From Proteopedia

Revision as of 03:29, 11 April 2020

Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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