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| | <StructureSection load='7zhg' size='340' side='right'caption='[[7zhg]], [[Resolution|resolution]] 2.25Å' scene=''> | | <StructureSection load='7zhg' size='340' side='right'caption='[[7zhg]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[7zhg]] is a 30 chain structure with sequence from [https://en.wikipedia.org/wiki/ ] and [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=7ZHG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZHG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7zhg]] 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=7ZHG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ZHG 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=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </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=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=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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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='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=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=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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7zhg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zhg OCA], [https://pdbe.org/7zhg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zhg RCSB], [https://www.ebi.ac.uk/pdbsum/7zhg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zhg 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=7zhg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7zhg OCA], [https://pdbe.org/7zhg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7zhg RCSB], [https://www.ebi.ac.uk/pdbsum/7zhg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7zhg ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/RS19_PYRAB RS19_PYRAB]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [[https://www.uniprot.org/uniprot/RS5_PYRAB RS5_PYRAB]] With S4 and S12 plays an important role in translational accuracy. [[https://www.uniprot.org/uniprot/RS14Z_PYRAB RS14Z_PYRAB]] Binds 16S rRNA, required for the assembly of 30S particles. [[https://www.uniprot.org/uniprot/RS19E_PYRAB RS19E_PYRAB]] May be involved in maturation of the 30S ribosomal subunit. [[https://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. [[https://www.uniprot.org/uniprot/RS10_PYRAB RS10_PYRAB]] Involved in the binding of tRNA to the ribosomes. [[https://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. [[https://www.uniprot.org/uniprot/RS3_PYRAB RS3_PYRAB]] Binds the lower part of the 30S subunit head. [[https://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. [[https://www.uniprot.org/uniprot/RS11_PYRAB RS11_PYRAB]] Located on the platform of the 30S subunit (By similarity). [[https://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. [[https://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] [[https://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. [[https://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/RS6E_PYRAB RS6E_PYRAB]] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 24: |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyrococcus abyssi ge5]] | + | [[Category: Pyrococcus abyssi GE5]] |
| - | [[Category: Bourgeois, G]] | + | [[Category: Bourgeois G]] |
| - | [[Category: Coureux, P D]] | + | [[Category: Coureux PD]] |
| - | [[Category: Kazan, R]] | + | [[Category: Kazan R]] |
| - | [[Category: Mechulam, Y]] | + | [[Category: Mechulam Y]] |
| - | [[Category: Schmitt, E]] | + | [[Category: Schmitt E]] |
| - | [[Category: Aif5b]]
| + | |
| - | [[Category: Initiation complex]]
| + | |
| - | [[Category: Small ribosomal subunit]]
| + | |
| - | [[Category: Translation]]
| + | |
| - | [[Category: Translation initiation]]
| + | |
| Structural highlights
7zhg is a 10 chain structure with sequence from Pyrococcus abyssi GE5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , , , , , , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[RS6E_PYRAB]
Publication Abstract from PubMed
In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 A resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.
Role of aIF5B in archaeal translation initiation.,Kazan R, Bourgeois G, Lazennec-Schurdevin C, Larquet E, Mechulam Y, Coureux PD, Schmitt E Nucleic Acids Res. 2022 Jun 24;50(11):6532-6548. doi: 10.1093/nar/gkac490. PMID:35694843[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kazan R, Bourgeois G, Lazennec-Schurdevin C, Larquet E, Mechulam Y, Coureux PD, Schmitt E. Role of aIF5B in archaeal translation initiation. Nucleic Acids Res. 2022 Jun 24;50(11):6532-6548. doi: 10.1093/nar/gkac490. PMID:35694843 doi:http://dx.doi.org/10.1093/nar/gkac490
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