|
|
| Line 3: |
Line 3: |
| | <SX load='5myj' size='340' side='right' viewer='molstar' caption='[[5myj]], [[Resolution|resolution]] 5.60Å' scene=''> | | <SX load='5myj' size='340' side='right' viewer='molstar' caption='[[5myj]], [[Resolution|resolution]] 5.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5myj]] is a 51 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._cremoris_(strain_mg1363) Lactococcus lactis subsp. cremoris (strain mg1363)] and [http://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._cremoris_mg1363 Lactococcus lactis subsp. cremoris mg1363]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MYJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MYJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5myj]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._cremoris_MG1363 Lactococcus lactis subsp. cremoris MG1363]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MYJ FirstGlance]. <br> |
| - | </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=5myj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5myj OCA], [http://pdbe.org/5myj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5myj RCSB], [http://www.ebi.ac.uk/pdbsum/5myj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5myj ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 5.6Å</td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5myj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5myj OCA], [https://pdbe.org/5myj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5myj RCSB], [https://www.ebi.ac.uk/pdbsum/5myj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5myj ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RL2_LACLM RL2_LACLM]] 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/RS7_LACLM RS7_LACLM]] 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/RS17_LACLM RS17_LACLM]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS18_LACLM RS18_LACLM]] 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/RL19_LACLM RL19_LACLM]] 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/RL15_LACLM RL15_LACLM]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RS14Z_LACLM RS14Z_LACLM]] 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/RS20_LACLM RS20_LACLM]] Binds directly to 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL24_LACLM RL24_LACLM]] 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/RS10_LACLM RS10_LACLM]] Involved in the binding of tRNA to the ribosomes. [[http://www.uniprot.org/uniprot/RL4_LACLM RL4_LACLM]] 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. Forms part of the polypeptide exit tunnel. [[http://www.uniprot.org/uniprot/RS11_LACLM RS11_LACLM]] 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/A2RNQ3_LACLM A2RNQ3_LACLM]] 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/RL21_LACLM RL21_LACLM]] This protein binds to 23S rRNA in the presence of protein L20. [[http://www.uniprot.org/uniprot/RS13_LACLM RS13_LACLM]] 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/RS6_LACLM RS6_LACLM]] Binds together with S18 to 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL14_LACLM RL14_LACLM]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [[http://www.uniprot.org/uniprot/RS3_LACLM RS3_LACLM]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. [[http://www.uniprot.org/uniprot/RL5_LACLM RL5_LACLM]] 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. [[http://www.uniprot.org/uniprot/HPF_LACLM HPF_LACLM]] Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase; 100S ribosomes are translationally inactive and sometimes present during exponential growth. Able to dimerize E.coli 70S ribosomes in vitro (PubMed:24279750).[HAMAP-Rule:MF_00839]<ref>PMID:24279750</ref> [[http://www.uniprot.org/uniprot/RL16_LACLM RL16_LACLM]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [[http://www.uniprot.org/uniprot/RS12_LACLM RS12_LACLM]] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403] 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] [[http://www.uniprot.org/uniprot/RL22_LACLM RL22_LACLM]] 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. [[http://www.uniprot.org/uniprot/RS15_LACLM RS15_LACLM]] 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/RS8_LACLM RS8_LACLM]] 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. [[http://www.uniprot.org/uniprot/A2RP62_LACLM A2RP62_LACLM]] 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][RuleBase:RU003878][SAAS:SAAS00725369] [[http://www.uniprot.org/uniprot/RS4_LACLM RS4_LACLM]] 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/RL3_LACLM RL3_LACLM]] 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/RL20_LACLM RL20_LACLM]] 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/RL6_LACLM RL6_LACLM]] 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/RL18_LACLM RL18_LACLM]] 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. [[http://www.uniprot.org/uniprot/RS19_LACLM RS19_LACLM]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS5_LACLM RS5_LACLM]] 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. | + | [https://www.uniprot.org/uniprot/RS2_LACLM RS2_LACLM] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 17: |
Line 18: |
| | </div> | | </div> |
| | <div class="pdbe-citations 5myj" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5myj" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| - | [[Category: Lactococcus lactis subsp. cremoris mg1363]] | + | [[Category: Lactococcus lactis subsp. cremoris MG1363]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Boekema, E J]] | + | [[Category: Boekema EJ]] |
| - | [[Category: Franken, L E]] | + | [[Category: Franken LE]] |
| - | [[Category: Guskov, A]] | + | [[Category: Guskov A]] |
| - | [[Category: Oostergetel, G T]] | + | [[Category: Oostergetel GT]] |
| - | [[Category: Pijning, T]] | + | [[Category: Pijning T]] |
| - | [[Category: Poolman, B]] | + | [[Category: Poolman B]] |
| - | [[Category: Puri, P]] | + | [[Category: Puri P]] |
| - | [[Category: Cryo-em]]
| + | |
| - | [[Category: Lactoccocus lacti]]
| + | |
| - | [[Category: Ribosome]]
| + | |
| Structural highlights
Function
RS2_LACLM
Publication Abstract from PubMed
Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we report the cryo-electron microscopy study on 100S ribosomes from Lactococcus lactis and a dimerization mechanism involving a single protein: HPFlong. The N-terminal domain of HPFlong binds at the same site as HPF in Escherichia coli 100S ribosomes. Contrary to ribosome modulation factor, the C-terminal domain of HPFlong binds exactly at the dimer interface. Furthermore, ribosomes from Lactococcus lactis do not undergo conformational changes in the 30S head domains upon binding of HPFlong, and the Shine-Dalgarno sequence and mRNA entrance tunnel remain accessible. Ribosome activity is blocked by HPFlong due to the inhibition of mRNA recognition by the platform binding center. Phylogenetic analysis of HPF proteins suggests that HPFlong-mediated dimerization is a widespread mechanism of ribosome hibernation in bacteria.When bacteria enter the stationary growth phase, protein translation is suppressed via the dimerization of 70S ribosomes into inactive complexes. Here the authors provide a structural basis for how the dual domain hibernation promotion factor promotes ribosome dimerization and hibernation in bacteria.
A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.,Franken LE, Oostergetel GT, Pijning T, Puri P, Arkhipova V, Boekema EJ, Poolman B, Guskov A Nat Commun. 2017 Sep 28;8(1):722. doi: 10.1038/s41467-017-00718-x. PMID:28959045[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Franken LE, Oostergetel GT, Pijning T, Puri P, Arkhipova V, Boekema EJ, Poolman B, Guskov A. A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy. Nat Commun. 2017 Sep 28;8(1):722. doi: 10.1038/s41467-017-00718-x. PMID:28959045 doi:http://dx.doi.org/10.1038/s41467-017-00718-x
|
