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| | <StructureSection load='4v85' size='340' side='right'caption='[[4v85]], [[Resolution|resolution]] 3.20Å' scene=''> | | <StructureSection load='4v85' size='340' side='right'caption='[[4v85]], [[Resolution|resolution]] 3.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4v85]] is a 59 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3sfs 3sfs] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3sgf 3sgf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V85 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V85 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4v85]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3sfs 3sfs] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3sgf 3sgf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V85 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V85 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <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=5OH:(2S)-AMINO[(4R,6S)-2-AMINO-6-HYDROXY-3,4,5,6-TETRAHYDROPYRIMIDIN-4-YL]ETHANOIC+ACID'>5OH</scene>, <scene name='pdbligand=DPP:DIAMINOPROPANOIC+ACID'>DPP</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=KBE:BETA-LYSINE'>KBE</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UAL:(2Z)-2-AMINO-3-(CARBAMOYLAMINO)PROP-2-ENOIC+ACID'>UAL</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5OH:(2S)-AMINO[(4R,6S)-2-AMINO-6-HYDROXY-3,4,5,6-TETRAHYDROPYRIMIDIN-4-YL]ETHANOIC+ACID'>5OH</scene>, <scene name='pdbligand=DPP:DIAMINOPROPANOIC+ACID'>DPP</scene>, <scene name='pdbligand=KBE:BETA-LYSINE'>KBE</scene>, <scene name='pdbligand=UAL:(2Z)-2-AMINO-3-(CARBAMOYLAMINO)PROP-2-ENOIC+ACID'>UAL</scene></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=4v85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v85 OCA], [https://pdbe.org/4v85 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v85 RCSB], [https://www.ebi.ac.uk/pdbsum/4v85 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v85 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b4375, JW5873, miaD, prfC, Termination Release Factor 3, tos ([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=4v85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v85 OCA], [http://pdbe.org/4v85 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v85 RCSB], [http://www.ebi.ac.uk/pdbsum/4v85 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v85 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/C3SQS2_ECOLX C3SQS2_ECOLX]] 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 (By similarity).[HAMAP-Rule:MF_00480] [[http://www.uniprot.org/uniprot/C3SQY7_ECOLX C3SQY7_ECOLX]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity).[SAAS:SAAS019979_004_007295][HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/C3SFP7_ECOLX C3SFP7_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 (By similarity).[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/C3SRX7_ECOLX C3SRX7_ECOLX]] 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:SAAS00012479] [[http://www.uniprot.org/uniprot/C3SQZ7_ECOLX C3SQZ7_ECOLX]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326] 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.[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/C3SR17_ECOLX C3SR17_ECOLX]] 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][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/RS20_ECOLI RS20_ECOLI]] Binds directly to 16S ribosomal RNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/C3SR07_ECOLX C3SR07_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 (By similarity).[HAMAP-Rule:MF_00537] [[http://www.uniprot.org/uniprot/C3SR22_ECOLX C3SR22_ECOLX]] 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/C3SQT7_ECOLX C3SQT7_ECOLX]] Involved in the binding of tRNA to the ribosomes (By similarity).[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/C3SR57_ECOLX C3SR57_ECOLX]] 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 (By similarity).[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/C3SQW7_ECOLX C3SQW7_ECOLX]] 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] 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.[HAMAP-Rule:MF_01331][RuleBase:RU004008] [[http://www.uniprot.org/uniprot/C3SIC7_ECOLX C3SIC7_ECOLX]] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.[HAMAP-Rule:MF_00736][RuleBase:RU003979][SAAS:SAAS00021701] [[http://www.uniprot.org/uniprot/C3SR37_ECOLX C3SR37_ECOLX]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00124822] [[http://www.uniprot.org/uniprot/C3SR52_ECOLX C3SR52_ECOLX]] 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 (By similarity).[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RF3_ECOLI RF3_ECOLI]] Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF-1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP.[HAMAP-Rule:MF_00072] [[http://www.uniprot.org/uniprot/C3SFQ7_ECOLX C3SFQ7_ECOLX]] Binds together with S18 to 16S ribosomal RNA (By similarity).[SAAS:SAAS020815_004_002222][HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/C3SYQ7_ECOLX C3SYQ7_ECOLX]] 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.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/C3SR02_ECOLX C3SR02_ECOLX]] 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/C3SQV7_ECOLX C3SQV7_ECOLX]] 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.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/C3SQX2_ECOLX C3SQX2_ECOLX]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity).[HAMAP-Rule:MF_01309] [[http://www.uniprot.org/uniprot/C3T7Q7_ECOLX C3T7Q7_ECOLX]] 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.[HAMAP-Rule:MF_00382][RuleBase:RU000560] [[http://www.uniprot.org/uniprot/C3SIB7_ECOLX C3SIB7_ECOLX]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors.[HAMAP-Rule:MF_00362][SAAS:SAAS00104953] [[http://www.uniprot.org/uniprot/C3SQR7_ECOLX C3SQR7_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 (By similarity).[RuleBase:RU003623][HAMAP-Rule:MF_00403] With S4 and S5 plays an important role in translational accuracy (By similarity).[RuleBase:RU003623][HAMAP-Rule:MF_00403] [[http://www.uniprot.org/uniprot/C3SQX7_ECOLX C3SQX7_ECOLX]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342][RuleBase:RU004414] [[http://www.uniprot.org/uniprot/C3SSQ7_ECOLX C3SSQ7_ECOLX]] Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity).[HAMAP-Rule:MF_01343] 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).[RuleBase:RU004524][HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/C3SSG2_ECOLX C3SSG2_ECOLX]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00030247] [[http://www.uniprot.org/uniprot/C3SQU7_ECOLX C3SQU7_ECOLX]] Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328] 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] [[http://www.uniprot.org/uniprot/C3SR12_ECOLX C3SR12_ECOLX]] 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 (By similarity).[HAMAP-Rule:MF_01302] [[http://www.uniprot.org/uniprot/C3SR62_ECOLX C3SR62_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 (By similarity).[HAMAP-Rule:MF_01306] With S5 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01306] [[http://www.uniprot.org/uniprot/C3T3H7_ECOLX C3T3H7_ECOLX]] 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_01336][SAAS:SAAS00148872] [[http://www.uniprot.org/uniprot/C3SQZ2_ECOLX C3SQZ2_ECOLX]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/C3SQU2_ECOLX C3SQU2_ECOLX]] 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.[HAMAP-Rule:MF_01325][RuleBase:RU003906] [[http://www.uniprot.org/uniprot/C3SIB2_ECOLX C3SIB2_ECOLX]] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors. Is thus essential for accurate translation.[HAMAP-Rule:MF_00368] [[http://www.uniprot.org/uniprot/C3SQW2_ECOLX C3SQW2_ECOLX]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/C3SQV2_ECOLX C3SQV2_ECOLX]] 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/C3SR27_ECOLX C3SR27_ECOLX]] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).[SAAS:SAAS005712_004_009826][HAMAP-Rule:MF_01307] With S4 and S12 plays an important role in translational accuracy (By similarity).[SAAS:SAAS005712_004_003902][HAMAP-Rule:MF_01307]
| + | [https://www.uniprot.org/uniprot/RS2_ECOLI RS2_ECOLI] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Lancaster, L]] | + | [[Category: Lancaster L]] |
| - | [[Category: Noller, H F]] | + | [[Category: Noller HF]] |
| - | [[Category: Trakhanov, S]] | + | [[Category: Trakhanov S]] |
| - | [[Category: Zhou, J]] | + | [[Category: Zhou J]] |
| - | [[Category: Ribosome-antibiotic complex]]
| + | |
| - | [[Category: Typeii release factor binding with ribosome]]
| + | |
