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| | <SX load='6qdw' size='340' side='right' viewer='molstar' caption='[[6qdw]], [[Resolution|resolution]] 2.83Å' scene=''> | | <SX load='6qdw' size='340' side='right' viewer='molstar' caption='[[6qdw]], [[Resolution|resolution]] 2.83Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6qdw]] is a 31 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin], [http://en.wikipedia.org/wiki/Ecobd Ecobd], [http://en.wikipedia.org/wiki/Escherichia_coli_(strain_b_/_bl21-de3) Escherichia coli (strain b / bl21-de3)] and [http://en.wikipedia.org/wiki/Escherichia_coli_bl21(de3) Escherichia coli bl21(de3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QDW OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6QDW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6qdw]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QDW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QDW FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CRYGB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])</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]] 2.83Å</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=6qdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qdw OCA], [http://pdbe.org/6qdw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qdw RCSB], [http://www.ebi.ac.uk/pdbsum/6qdw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qdw 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=6qdw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qdw OCA], [https://pdbe.org/6qdw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qdw RCSB], [https://www.ebi.ac.uk/pdbsum/6qdw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qdw ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CRGB_BOVIN CRGB_BOVIN]] Crystallins are the dominant structural components of the vertebrate eye lens. [[http://www.uniprot.org/uniprot/A0A140N7J1_ECOBD A0A140N7J1_ECOBD]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome.[HAMAP-Rule:MF_01320] [[http://www.uniprot.org/uniprot/A0A140N2S3_ECOBD A0A140N2S3_ECOBD]] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome.[HAMAP-Rule:MF_01331] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g., L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01331][RuleBase:RU004008] [[http://www.uniprot.org/uniprot/A0A140N598_ECOBD A0A140N598_ECOBD]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly.[HAMAP-Rule:MF_01366][RuleBase:RU003878][SAAS:SAAS00725369] [[http://www.uniprot.org/uniprot/A0A140N4L0_ECOBD A0A140N4L0_ECOBD]] This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.[HAMAP-Rule:MF_01337] [[http://www.uniprot.org/uniprot/A0A140N3H4_ECOBD A0A140N3H4_ECOBD]] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome.[HAMAP-Rule:MF_01367][RuleBase:RU003950] [[http://www.uniprot.org/uniprot/A0A140N846_ECOBD A0A140N846_ECOBD]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01336][SAAS:SAAS01080239] [[http://www.uniprot.org/uniprot/A0A140N6T7_ECOBD A0A140N6T7_ECOBD]] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site.[HAMAP-Rule:MF_00402][RuleBase:RU000559] [[http://www.uniprot.org/uniprot/A0A140NDV1_ECOBD A0A140NDV1_ECOBD]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/A0A140N5K8_ECOBD A0A140N5K8_ECOBD]] Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.[HAMAP-Rule:MF_01328] [[http://www.uniprot.org/uniprot/C6EGE8_ECOBD C6EGE8_ECOBD]] One of the early assembly proteins it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/A0A140N5D7_ECOBD A0A140N5D7_ECOBD]] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363][RuleBase:RU000562][SAAS:SAAS00352917] [[http://www.uniprot.org/uniprot/A0A140N5L7_ECOBD A0A140N5L7_ECOBD]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01326] [[http://www.uniprot.org/uniprot/A0A140N3G7_ECOBD A0A140N3G7_ECOBD]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit.[HAMAP-Rule:MF_01325][RuleBase:RU003906] [[http://www.uniprot.org/uniprot/A0A140N6Z2_ECOBD A0A140N6Z2_ECOBD]] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs.[HAMAP-Rule:MF_01342][RuleBase:RU004414] [[http://www.uniprot.org/uniprot/A0A140N5A3_ECOBD A0A140N5A3_ECOBD]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333] [[http://www.uniprot.org/uniprot/A0A140N2T1_ECOBD A0A140N2T1_ECOBD]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365][RuleBase:RU003870] [[http://www.uniprot.org/uniprot/A0A140NBS1_ECOBD A0A140NBS1_ECOBD]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit.[HAMAP-Rule:MF_00382][RuleBase:RU000560] [[http://www.uniprot.org/uniprot/A0A140N711_ECOBD A0A140N711_ECOBD]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00124822] | + | [https://www.uniprot.org/uniprot/RL28_ECOLI RL28_ECOLI] |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein gammaB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding. |
| | + | |
| | + | Cysteine oxidation and disulfide formation in the ribosomal exit tunnel.,Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau VV, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H Nat Commun. 2020 Nov 4;11(1):5569. doi: 10.1038/s41467-020-19372-x. PMID:33149120<ref>PMID:33149120</ref> |
| | + | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 6qdw" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| | *[[Crystallin 3D structures|Crystallin 3D structures]] | | *[[Crystallin 3D structures|Crystallin 3D structures]] |
| | + | == References == |
| | + | <references/> |
| | __TOC__ | | __TOC__ |
| | </SX> | | </SX> |
| - | [[Category: Bovin]] | |
| - | [[Category: Ecobd]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Frangakis, A]] | + | [[Category: Frangakis A]] |
| - | [[Category: Glaubitz, C]] | + | [[Category: Glaubitz C]] |
| - | [[Category: Hodirnau, V V]] | + | [[Category: Hodirnau VV]] |
| - | [[Category: Kudlinzki, D]] | + | [[Category: Kudlinzki D]] |
| - | [[Category: Mao, J]] | + | [[Category: Mao J]] |
| - | [[Category: Reitz, J]] | + | [[Category: Reitz J]] |
| - | [[Category: Schulte, L]] | + | [[Category: Schulte L]] |
| - | [[Category: Schwalbe, H]] | + | [[Category: Schwalbe H]] |
| - | [[Category: 50s ribosome]]
| + | |
| - | [[Category: Nascent peptide chain]]
| + | |
| - | [[Category: Ribosome]]
| + | |
| - | [[Category: Translation]]
| + | |
| Structural highlights
Function
RL28_ECOLI
Publication Abstract from PubMed
Understanding the conformational sampling of translation-arrested ribosome nascent chain complexes is key to understand co-translational folding. Up to now, coupling of cysteine oxidation, disulfide bond formation and structure formation in nascent chains has remained elusive. Here, we investigate the eye-lens protein gammaB-crystallin in the ribosomal exit tunnel. Using mass spectrometry, theoretical simulations, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance and cryo-electron microscopy, we show that thiol groups of cysteine residues undergo S-glutathionylation and S-nitrosylation and form non-native disulfide bonds. Thus, covalent modification chemistry occurs already prior to nascent chain release as the ribosome exit tunnel provides sufficient space even for disulfide bond formation which can guide protein folding.
Cysteine oxidation and disulfide formation in the ribosomal exit tunnel.,Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau VV, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H Nat Commun. 2020 Nov 4;11(1):5569. doi: 10.1038/s41467-020-19372-x. PMID:33149120[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau VV, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H. Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nat Commun. 2020 Nov 4;11(1):5569. PMID:33149120 doi:10.1038/s41467-020-19372-x
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