6tmf

From Proteopedia

(Difference between revisions)

Revision as of 06:31, 11 April 2020

Structure of an archaeal ABCE1-bound ribosomal post-splitting complex

6tmf, resolution 2.80Å

Structural highlights

6tmf is a 30 chain structure with sequence from Thermococcus celer dsm 2476 and Thermococcus celer vu 13 = jcm 8558. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	SSOP1_0270, SULA_1305, SULB_1306, SULC_1304, SULG_06465, SULH_06465, SULI_06465, SULM_06465, SULN_06465, SULO_06475, SULZ_06710 (Thermococcus celer DSM 2476)
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[A0A218P4M9_THECE] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA.[HAMAP-Rule:MF_00531] [A0A218P4N5_THECE] With S4 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01307] [A0A218NZW1_THECE] Binds 16S rRNA, required for the assembly of 30S particles.[HAMAP-Rule:MF_01364] [A0A218P4W7_THECE] May be involved in maturation of the 30S ribosomal subunit.[HAMAP-Rule:MF_01474] [A0A218P3Q8_THECE] Involved in the binding of tRNA to the ribosomes.[HAMAP-Rule:MF_00508][SAAS:SAAS00243318] [A0A218NZT2_THECE] 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.[HAMAP-Rule:MF_01315] [A0A218P167_THECE] 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.[HAMAP-Rule:MF_00326] [A0A218NZU7_THECE] Binds the lower part of the 30S subunit head.[HAMAP-Rule:MF_01309] [A0A218P4K4_THECE] 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.[HAMAP-Rule:MF_00480] [A0A218NZU0_THECE] Located on the platform of the 30S subunit.[HAMAP-Rule:MF_01310] [A0A218P4I2_THECE] With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits.[HAMAP-Rule:MF_00403][RuleBase:RU004490] [A0A218NZT7_THECE] 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.[HAMAP-Rule:MF_01302] [A0A218NZX3_THECE] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.[HAMAP-Rule:MF_01345] [A0A218NZV3_THECE] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit.[HAMAP-Rule:MF_01306][SAAS:SAAS00896430] With S5 and S12 plays an important role in translational accuracy.[HAMAP-Rule:MF_01306][SAAS:SAAS00896433]

Publication Abstract from PubMed

Ribosome recycling by the twin-ATPase ABCE1 is a key regulatory process in mRNA translation and surveillance and in ribosome-associated protein quality control in Eukarya and Archaea. Here, we captured the archaeal 30S ribosome post-splitting complex at 2.8 A resolution by cryo-electron microscopy. The structure reveals the dynamic behavior of structural motifs unique to ABCE1, which ultimately leads to ribosome splitting. More specifically, we provide molecular details on how conformational rearrangements of the iron-sulfur cluster domain and hinge regions of ABCE1 are linked to closure of its nucleotide-binding sites. The combination of mutational and functional analyses uncovers an intricate allosteric network between the ribosome, regulatory domains of ABCE1, and its two structurally and functionally asymmetric ATP-binding sites. Based on these data, we propose a refined model of how signals from the ribosome are integrated into the ATPase cycle of ABCE1 to orchestrate ribosome recycling.

Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex.,Nurenberg-Goloub E, Kratzat H, Heinemann H, Heuer A, Kotter P, Berninghausen O, Becker T, Tampe R, Beckmann R EMBO J. 2020 Feb 17:e103788. doi: 10.15252/embj.2019103788. PMID:32064661^[1]

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

References

↑ Nurenberg-Goloub E, Kratzat H, Heinemann H, Heuer A, Kotter P, Berninghausen O, Becker T, Tampe R, Beckmann R. Molecular analysis of the ribosome recycling factor ABCE1 bound to the 30S post-splitting complex. EMBO J. 2020 Feb 17:e103788. doi: 10.15252/embj.2019103788. PMID:32064661 doi:http://dx.doi.org/10.15252/embj.2019103788

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/6tmf"

@@ Line 3: / Line 3: @@
 <SX load='6tmf' size='340' side='right' viewer='molstar' caption='[[6tmf]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6tmf]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_celer_dsm_2476 Thermococcus celer dsm 2476] and [http://en.wikipedia.org/wiki/Thermococcus_celer_vu_13_=_jcm_8558 Thermococcus celer vu 13 = jcm 8558]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6TMF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6tmf]] is a 30 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermococcus_celer_dsm_2476 Thermococcus celer dsm 2476] and [http://en.wikipedia.org/wiki/Thermococcus_celer_vu_13_=_jcm_8558 Thermococcus celer vu 13 = jcm 8558]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TMF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TMF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SSOP1_0270, SULA_1305, SULB_1306, SULC_1304, SULG_06465, SULH_06465, SULI_06465, SULM_06465, SULN_06465, SULO_06475, SULZ_06710 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1293037 Thermococcus celer DSM 2476])</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=6tmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tmf OCA], [http://pdbe.org/6tmf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tmf RCSB], [http://www.ebi.ac.uk/pdbsum/6tmf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tmf 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=6tmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tmf OCA], [http://pdbe.org/6tmf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tmf RCSB], [http://www.ebi.ac.uk/pdbsum/6tmf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tmf ProSAT]</span></td></tr>
 </table>
 == Function ==

6tmf

From Proteopedia

Revision as of 06:31, 11 April 2020

Structure of an archaeal ABCE1-bound ribosomal post-splitting complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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