5jb3

From Proteopedia

(Difference between revisions)

Revision as of 20:21, 10 April 2020

Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-REMOTE conformation

5jb3, resolution 5.34Å

Structural highlights

5jb3 is a 35 chain structure with sequence from [1], Pyrab and Pyrococcus abyssi ge5. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	MJ0463 (PYRAB), eIF1A, aif1A, PYRAB05910, PAB2441 (PYRAB), eif2g, SSO0412 (PYRAB), eif2b, aif2b, SSO2381 (PYRAB), eif2a, aif2a, SSO1050 (PYRAB)
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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). [RS14Z_PYRAB] Binds 16S rRNA, required for the assembly of 30S particles. [RS11_PYRAB] Located on the platform of the 30S subunit (By similarity). [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. [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. [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. [RS19E_PYRAB] May be involved in maturation of the 30S ribosomal subunit. [RS3_PYRAB] Binds the lower part of the 30S subunit head. [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. [RS5_PYRAB] With S4 and S12 plays an important role in translational accuracy. [RS19_PYRAB] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [RS12_PYRAB] With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits. [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. [RS10_PYRAB] Involved in the binding of tRNA to the ribosomes. [RS17_PYRAB] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.[HAMAP-Rule:MF_01345]

Publication Abstract from PubMed

Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNAiMet) and mRNA bound to the small ribosomal subunit. e/aIF2 plays a crucial role in this process but how this factor controls start codon selection remains unclear. Here, we present cryo-EM structures of the full archaeal 30S initiation complex showing two conformational states of the TC. In the first state, the TC is bound to the ribosome in a relaxed conformation with the tRNA oriented out of the P site. In the second state, the tRNA is accommodated within the peptidyl (P) site and the TC becomes constrained. This constraint is compensated by codon/anticodon base pairing, whereas in the absence of a start codon, aIF2 contributes to swing out the tRNA. This spring force concept highlights a mechanism of codon/anticodon probing by the initiator tRNA directly assisted by aIF2.

Cryo-EM study of start codon selection during archaeal translation initiation.,Coureux PD, Lazennec-Schurdevin C, Monestier A, Larquet E, Cladiere L, Klaholz BP, Schmitt E, Mechulam Y Nat Commun. 2016 Nov 7;7:13366. doi: 10.1038/ncomms13366. PMID:27819266^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Coureux PD, Lazennec-Schurdevin C, Monestier A, Larquet E, Cladiere L, Klaholz BP, Schmitt E, Mechulam Y. Cryo-EM study of start codon selection during archaeal translation initiation. Nat Commun. 2016 Nov 7;7:13366. doi: 10.1038/ncomms13366. PMID:27819266 doi:http://dx.doi.org/10.1038/ncomms13366

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5jb3"

@@ Line 3: / Line 3: @@
 <SX load='5jb3' size='340' side='right' viewer='molstar' caption='[[5jb3]], [[Resolution|resolution]] 5.34&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5jb3]] is a 35 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Pyrab Pyrab] 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=5JB3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JB3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5jb3]] is a 35 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Pyrab Pyrab] 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=5JB3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JB3 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ0463 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB]), eIF1A, aif1A, PYRAB05910, PAB2441 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB]), eif2g, SSO0412 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB]), eif2b, aif2b, SSO2381 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB]), eif2a, aif2a, SSO1050 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</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=5jb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jb3 OCA], [http://pdbe.org/5jb3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jb3 RCSB], [http://www.ebi.ac.uk/pdbsum/5jb3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jb3 ProSAT]</span></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=5jb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jb3 OCA], [http://pdbe.org/5jb3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jb3 RCSB], [http://www.ebi.ac.uk/pdbsum/5jb3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jb3 ProSAT]</span></td></tr>
 </table>
 == Function ==

5jb3

From Proteopedia

Revision as of 20:21, 10 April 2020

Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-REMOTE conformation

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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