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| | <SX load='6v3a' size='340' side='right' viewer='molstar' caption='[[6v3a]], [[Resolution|resolution]] 2.82Å' scene=''> | | <SX load='6v3a' size='340' side='right' viewer='molstar' caption='[[6v3a]], [[Resolution|resolution]] 2.82Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6v3a]] is a 52 chain structure with sequence from [http://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii], [http://en.wikipedia.org/wiki/Acinetobacter_baumannii_(strain_ab0057) Acinetobacter baumannii (strain ab0057)], [http://en.wikipedia.org/wiki/Acinetobacter_baumannii_ab0057 Acinetobacter baumannii ab0057], [http://en.wikipedia.org/wiki/Acinetobacter_beijerinckii_anc_3835 Acinetobacter beijerinckii anc 3835], [http://en.wikipedia.org/wiki/Acinetobacter_rudis_cip_110305 Acinetobacter rudis cip 110305], [http://en.wikipedia.org/wiki/Acinetobacter_sp._263903-1 Acinetobacter sp. 263903-1], [http://en.wikipedia.org/wiki/Acinetobacter_sp._809848 Acinetobacter sp. 809848], [http://en.wikipedia.org/wiki/Acinetobacter_sp._anc_4470 Acinetobacter sp. anc 4470], [http://en.wikipedia.org/wiki/Acinetobacter_sp._anc_5600 Acinetobacter sp. anc 5600], [http://en.wikipedia.org/wiki/Acinetobacter_sp._cip_102082 Acinetobacter sp. cip 102082], [http://en.wikipedia.org/wiki/Acinetobacter_sp._cip_51.11 Acinetobacter sp. cip 51.11], [http://en.wikipedia.org/wiki/Acinetobacter_sp._niph_899 Acinetobacter sp. niph 899] and [http://en.wikipedia.org/wiki/Acinetobacter_venetianus Acinetobacter venetianus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V3A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6V3A FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6v3a]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii], [https://en.wikipedia.org/wiki/Acinetobacter_baumannii_AB0057 Acinetobacter baumannii AB0057] and [https://en.wikipedia.org/wiki/Acinetobacter_variabilis Acinetobacter variabilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6V3A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6V3A FirstGlance]. <br> |
| - | </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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 2.82Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3TD:(1S)-1,4-ANHYDRO-1-(3-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-5-O-PHOSPHONO-D-RIBITOL'>3TD</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3TD:(1S)-1,4-ANHYDRO-1-(3-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-5-O-PHOSPHONO-D-RIBITOL'>3TD</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=6v3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v3a OCA], [http://pdbe.org/6v3a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6v3a RCSB], [http://www.ebi.ac.uk/pdbsum/6v3a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6v3a ProSAT]</span></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=6v3a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6v3a OCA], [https://pdbe.org/6v3a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6v3a RCSB], [https://www.ebi.ac.uk/pdbsum/6v3a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6v3a ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/V5V9N0_ACIBA V5V9N0_ACIBA]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309] [[http://www.uniprot.org/uniprot/RL21_ACIB5 RL21_ACIB5]] This protein binds to 23S rRNA in the presence of protein L20. [[http://www.uniprot.org/uniprot/RL2_ACIB5 RL2_ACIB5]] 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/RL18_ACIB5 RL18_ACIB5]] 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/RL16_ACIB5 RL16_ACIB5]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [[http://www.uniprot.org/uniprot/RS14_ACIB5 RS14_ACIB5]] 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/RL25_ACIB5 RL25_ACIB5]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance. [[http://www.uniprot.org/uniprot/A0A1T1GZ10_9GAMM A0A1T1GZ10_9GAMM]] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/N8WQT6_9GAMM N8WQT6_9GAMM]] 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/V5VGC9_ACIBA V5VGC9_ACIBA]] 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/RS19_ACIB5 RS19_ACIB5]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL24_ACIB5 RL24_ACIB5]] 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/RL5_ACIB5 RL5_ACIB5]] 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/RS5_ACIB5 RS5_ACIB5]] 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. [[http://www.uniprot.org/uniprot/RL6_ACIB5 RL6_ACIB5]] 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/A0A150HZL5_9GAMM A0A150HZL5_9GAMM]] 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] [[http://www.uniprot.org/uniprot/RS12_ACIB5 RS12_ACIB5]] 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/A0A009QSN8_9GAMM A0A009QSN8_9GAMM]] 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/RL13_ACIB5 RL13_ACIB5]] 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. [[http://www.uniprot.org/uniprot/RL23_ACIB5 RL23_ACIB5]] 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. [[http://www.uniprot.org/uniprot/RS20_ACIB5 RS20_ACIB5]] Binds directly to 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS6_ACIB5 RS6_ACIB5]] Binds together with S18 to 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL4_ACIB5 RL4_ACIB5]] 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/A0A062C259_9GAMM A0A062C259_9GAMM]] 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.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RL9_ACIB5 RL9_ACIB5]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RS17_ACIB5 RS17_ACIB5]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RL15_ACIB5 RL15_ACIB5]] Binds to the 23S rRNA. [[http://www.uniprot.org/uniprot/RL3_ACIB5 RL3_ACIB5]] 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/RS8_ACIB5 RS8_ACIB5]] 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/RS4_ACIB5 RS4_ACIB5]] 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/RS15_ACIB5 RS15_ACIB5]] 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. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome. [[http://www.uniprot.org/uniprot/RS7_ACIB5 RS7_ACIB5]] 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/RS13_ACIB5 RS13_ACIB5]] 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/RL19_ACIB5 RL19_ACIB5]] 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. | + | [https://www.uniprot.org/uniprot/RL2_ACIB5 RL2_ACIB5] 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. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6v3a" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6v3a" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Ribosome 3D structures|Ribosome 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </SX> | | </SX> |
| | [[Category: Acinetobacter baumannii]] | | [[Category: Acinetobacter baumannii]] |
| - | [[Category: Acinetobacter baumannii ab0057]] | + | [[Category: Acinetobacter baumannii AB0057]] |
| - | [[Category: Acinetobacter beijerinckii anc 3835]] | + | [[Category: Acinetobacter variabilis]] |
| - | [[Category: Acinetobacter rudis cip 110305]]
| + | |
| - | [[Category: Acinetobacter sp. 263903-1]]
| + | |
| - | [[Category: Acinetobacter sp. 809848]]
| + | |
| - | [[Category: Acinetobacter sp. anc 4470]]
| + | |
| - | [[Category: Acinetobacter sp. anc 5600]]
| + | |
| - | [[Category: Acinetobacter sp. cip 102082]]
| + | |
| - | [[Category: Acinetobacter sp. cip 51 11]]
| + | |
| - | [[Category: Acinetobacter sp. niph 899]]
| + | |
| - | [[Category: Acinetobacter venetianus]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Morgan, C E]] | + | [[Category: Morgan CE]] |
| - | [[Category: Yu, E W]] | + | [[Category: Yu EW]] |
| - | [[Category: Ribosome]]
| + | |
