6rw4

From Proteopedia

(Difference between revisions)

Current revision

Structure of human mitochondrial 28S ribosome in complex with mitochondrial IF3

Structural highlights

6rw4 is a 31 chain structure with sequence from Human and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , , , ,
NonStd Res:	, , , ,
Gene:	MTIF3, DC38 (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

[RT22_HUMAN] Hypotonia with lactic acidemia and hyperammonemia. The disease is caused by mutations affecting the gene represented in this entry. [RT16_HUMAN] Combined oxidative phosphorylation defect type 2. The disease is caused by mutations affecting the gene represented in this entry.

Function

[IF3M_HUMAN] IF-3 binds to the 28S ribosomal subunit and shifts the equilibrum between 55S ribosomes and their 39S and 28S subunits in favor of the free subunits, thus enhancing the availability of 28S subunits on which protein synthesis initiation begins.^[1] [AKIP_HUMAN] May act as a negative regulator of Aurora-A kinase, by down-regulation through proteasome-dependent degradation. [RT29_HUMAN] Involved in mediating interferon-gamma-induced cell death. [PTCD3_HUMAN] Mitochondrial RNA-binding protein that has a role in mitochondrial translation.^[2]

Publication Abstract from PubMed

Translation initiation in human mitochondria relies upon specialized mitoribosomes and initiation factors, mtIF2 and mtIF3, which have diverged from their bacterial counterparts. Here we report two distinct mitochondrial pre-initiation assembly steps involving those factors. Single-particle cryo-EM revealed that in the first step, interactions between mitochondria-specific protein mS37 and mtIF3 keep the small mitoribosomal subunit in a conformation favorable for a subsequent accommodation of mtIF2 in the second step. Combination with fluorescence cross-correlation spectroscopy analyses suggests that mtIF3 promotes complex assembly without mRNA or initiator tRNA binding, where exclusion is achieved by the N-terminal and C-terminal domains of mtIF3. Finally, the association of large mitoribosomal subunit is required for initiator tRNA and leaderless mRNA recruitment to form a stable initiation complex. These data reveal fundamental aspects of mammalian protein synthesis that are specific to mitochondria.

Distinct pre-initiation steps in human mitochondrial translation.,Khawaja A, Itoh Y, Remes C, Spahr H, Yukhnovets O, Hofig H, Amunts A, Rorbach J Nat Commun. 2020 Jun 10;11(1):2932. doi: 10.1038/s41467-020-16503-2. PMID:32522994^[3]

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

References

↑ Koc EC, Spremulli LL. Identification of mammalian mitochondrial translational initiation factor 3 and examination of its role in initiation complex formation with natural mRNAs. J Biol Chem. 2002 Sep 20;277(38):35541-9. doi: 10.1074/jbc.M202498200. Epub 2002 , Jul 2. PMID:12095986 doi:http://dx.doi.org/10.1074/jbc.M202498200
↑ Davies SM, Rackham O, Shearwood AM, Hamilton KL, Narsai R, Whelan J, Filipovska A. Pentatricopeptide repeat domain protein 3 associates with the mitochondrial small ribosomal subunit and regulates translation. FEBS Lett. 2009 Jun 18;583(12):1853-8. Epub 2009 May 8. PMID:19427859 doi:http://dx.doi.org/S0014-5793(09)00357-3
↑ Khawaja A, Itoh Y, Remes C, Spahr H, Yukhnovets O, Hofig H, Amunts A, Rorbach J. Distinct pre-initiation steps in human mitochondrial translation. Nat Commun. 2020 Jun 10;11(1):2932. doi: 10.1038/s41467-020-16503-2. PMID:32522994 doi:http://dx.doi.org/10.1038/s41467-020-16503-2

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6rw4"

@@ Line 3: / Line 3: @@
 <StructureSection load='6rw4' size='340' side='right'caption='[[6rw4]], [[Resolution|resolution]] 2.97&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6rw4]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RW4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RW4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6rw4]] is a 31 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RW4 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=SRY:STREPTOMYCIN'>SRY</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=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=AYA:N-ACETYLALANINE'>AYA</scene>, <scene name='pdbligand=B8T:'>B8T</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MTIF3, DC38 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MTIF3, DC38 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6rw4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rw4 OCA], [http://pdbe.org/6rw4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rw4 RCSB], [http://www.ebi.ac.uk/pdbsum/6rw4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rw4 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=6rw4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rw4 OCA], [https://pdbe.org/6rw4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rw4 RCSB], [https://www.ebi.ac.uk/pdbsum/6rw4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rw4 ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/RT22_HUMAN RT22_HUMAN]] Hypotonia with lactic acidemia and hyperammonemia. The disease is caused by mutations affecting the gene represented in this entry. [[http://www.uniprot.org/uniprot/RT16_HUMAN RT16_HUMAN]] Combined oxidative phosphorylation defect type 2. The disease is caused by mutations affecting the gene represented in this entry.
+[[https://www.uniprot.org/uniprot/RT22_HUMAN RT22_HUMAN]] Hypotonia with lactic acidemia and hyperammonemia. The disease is caused by mutations affecting the gene represented in this entry. [[https://www.uniprot.org/uniprot/RT16_HUMAN RT16_HUMAN]] Combined oxidative phosphorylation defect type 2. The disease is caused by mutations affecting the gene represented in this entry.
 == Function ==
-[[http://www.uniprot.org/uniprot/IF3M_HUMAN IF3M_HUMAN]] IF-3 binds to the 28S ribosomal subunit and shifts the equilibrum between 55S ribosomes and their 39S and 28S subunits in favor of the free subunits, thus enhancing the availability of 28S subunits on which protein synthesis initiation begins.<ref>PMID:12095986</ref>  [[http://www.uniprot.org/uniprot/AKIP_HUMAN AKIP_HUMAN]] May act as a negative regulator of Aurora-A kinase, by down-regulation through proteasome-dependent degradation. [[http://www.uniprot.org/uniprot/RT29_HUMAN RT29_HUMAN]] Involved in mediating interferon-gamma-induced cell death. [[http://www.uniprot.org/uniprot/PTCD3_HUMAN PTCD3_HUMAN]] Mitochondrial RNA-binding protein that has a role in mitochondrial translation.<ref>PMID:19427859</ref>
+[[https://www.uniprot.org/uniprot/IF3M_HUMAN IF3M_HUMAN]] IF-3 binds to the 28S ribosomal subunit and shifts the equilibrum between 55S ribosomes and their 39S and 28S subunits in favor of the free subunits, thus enhancing the availability of 28S subunits on which protein synthesis initiation begins.<ref>PMID:12095986</ref>  [[https://www.uniprot.org/uniprot/AKIP_HUMAN AKIP_HUMAN]] May act as a negative regulator of Aurora-A kinase, by down-regulation through proteasome-dependent degradation. [[https://www.uniprot.org/uniprot/RT29_HUMAN RT29_HUMAN]] Involved in mediating interferon-gamma-induced cell death. [[https://www.uniprot.org/uniprot/PTCD3_HUMAN PTCD3_HUMAN]] Mitochondrial RNA-binding protein that has a role in mitochondrial translation.<ref>PMID:19427859</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==

6rw4

From Proteopedia

Current revision

Structure of human mitochondrial 28S ribosome in complex with mitochondrial IF3

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

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