|
|
| (One intermediate revision not shown.) |
| Line 3: |
Line 3: |
| | <SX load='6sw9' size='340' side='right' viewer='molstar' caption='[[6sw9]], [[Resolution|resolution]] 4.20Å' scene=''> | | <SX load='6sw9' size='340' side='right' viewer='molstar' caption='[[6sw9]], [[Resolution|resolution]] 4.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6sw9]] is a 34 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Pyrococcus_abyssi_ge5 Pyrococcus abyssi ge5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SW9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6sw9]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SW9 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=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 4.2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4AC:N(4)-ACETYLCYTIDINE-5-MONOPHOSPHATE'>4AC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5HM:5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HM</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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=B8H:'>B8H</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=LHH:'>LHH</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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=4AC:N(4)-ACETYLCYTIDINE-5-MONOPHOSPHATE'>4AC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5HM:5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HM</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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=B8H:[(2~{R},3~{S},4~{R},5~{S})-5-[1-methyl-2,4-bis(oxidanylidene)pyrimidin-5-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>B8H</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=LHH:[(2~{R},3~{R},4~{R},5~{R})-5-(4-acetamido-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl+dihydrogen+phosphate'>LHH</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6sw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sw9 OCA], [http://pdbe.org/6sw9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6sw9 RCSB], [http://www.ebi.ac.uk/pdbsum/6sw9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6sw9 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=6sw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6sw9 OCA], [https://pdbe.org/6sw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6sw9 RCSB], [https://www.ebi.ac.uk/pdbsum/6sw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6sw9 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/IF2G_SACS2 IF2G_SACS2]] eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA.[HAMAP-Rule:MF_00119] [[http://www.uniprot.org/uniprot/IF1A_PYRAB IF1A_PYRAB]] Seems to be required for maximal rate of protein biosynthesis. Enhances ribosome dissociation into subunits and stabilizes the binding of the initiator Met-tRNA(I) to 40 S ribosomal subunits (By similarity). [[http://www.uniprot.org/uniprot/RS19_PYRAB RS19_PYRAB]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS5_PYRAB RS5_PYRAB]] With S4 and S12 plays an important role in translational accuracy. [[http://www.uniprot.org/uniprot/RS14Z_PYRAB RS14Z_PYRAB]] Binds 16S rRNA, required for the assembly of 30S particles. [[http://www.uniprot.org/uniprot/RS13_PYRAB RS13_PYRAB]] 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. [[http://www.uniprot.org/uniprot/RS3_PYRAB RS3_PYRAB]] Binds the lower part of the 30S subunit head. [[http://www.uniprot.org/uniprot/RS11_PYRAB RS11_PYRAB]] Located on the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS8_PYRAB RS8_PYRAB]] 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/IF2A_SACS2 IF2A_SACS2]] eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA.[HAMAP-Rule:MF_00231] [[http://www.uniprot.org/uniprot/RS19E_PYRAB RS19E_PYRAB]] May be involved in maturation of the 30S ribosomal subunit. [[http://www.uniprot.org/uniprot/RS10_PYRAB RS10_PYRAB]] Involved in the binding of tRNA to the ribosomes. [[http://www.uniprot.org/uniprot/RL7A_PYRAB RL7A_PYRAB]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs. [[http://www.uniprot.org/uniprot/RS7_PYRAB RS7_PYRAB]] 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. [[http://www.uniprot.org/uniprot/RS12_PYRAB RS12_PYRAB]] With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits. [[http://www.uniprot.org/uniprot/IF2B_SACS2 IF2B_SACS2]] eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA.[HAMAP-Rule:MF_00232] [[http://www.uniprot.org/uniprot/RS17_PYRAB RS17_PYRAB]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/RS4_PYRAB RS4_PYRAB]] 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. | + | [https://www.uniprot.org/uniprot/RS3A_PYRAB RS3A_PYRAB] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 24: |
Line 24: |
| | </SX> | | </SX> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyrococcus abyssi ge5]] | + | [[Category: Pyrococcus abyssi GE5]] |
| - | [[Category: Coureux, P D]] | + | [[Category: Coureux P-D]] |
| - | [[Category: Mechulam, Y]] | + | [[Category: Mechulam Y]] |
| - | [[Category: Schmitt, E]] | + | [[Category: Schmitt E]] |
| - | [[Category: Archaea]]
| + | |
| - | [[Category: Cryo-em]]
| + | |
| - | [[Category: Evolution]]
| + | |
| - | [[Category: Ribosome]]
| + | |
| - | [[Category: Rrna modification]]
| + | |
| - | [[Category: Translation initiation]]
| + | |
| - | [[Category: Trna]]
| + | |
