7jl3: Difference between revisions

Revision as of 14:52, 6 March 2024

Cryo-EM structure of RIG-I:dsRNA filament in complex with RIPLET PrySpry domain (trimer)

Structural highlights

7jl3 is a 8 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 4.2Å
Ligands:	ADP, ALF, MG, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

RN135_HUMAN Overgrowth-macrocephaly-facial dysmorphism syndrome.

Function

RN135_HUMAN E2-dependent E3 ubiquitin-protein ligase that functions as a RIGI coreceptor in the sensing of viral RNAs in cell cytoplasm and the activation of the antiviral innate immune response (PubMed:19017631, PubMed:19484123, PubMed:21147464, PubMed:23950712, PubMed:28469175, PubMed:31006531). Together with the UBE2D3, UBE2N and UB2V1 E2 ligases, catalyzes the 'Lys-63'-linked polyubiquitination of RIGI oligomerized on viral RNAs, an essential step in the activation of the RIG-I signaling pathway (PubMed:19017631, PubMed:21147464, PubMed:28469175, PubMed:31006531). Through a ubiquitin-independent parallel mechanism, which consists in bridging RIGI filaments forming on longer viral RNAs, further activates the RIG-I signaling pathway (PubMed:31006531). This second mechanism that synergizes with the ubiquitin-dependent one would thereby allow an RNA length-dependent regulation of the RIG-I signaling pathway (Probable). Associated with the E2 ligase UBE2N, also constitutively synthesizes unanchored 'Lys-63'-linked polyubiquitin chains that may also activate the RIG-I signaling pathway (PubMed:28469175, PubMed:31006531).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7]

References

↑ Oshiumi H, Matsumoto M, Hatakeyama S, Seya T. Riplet/RNF135, a RING finger protein, ubiquitinates RIG-I to promote interferon-beta induction during the early phase of viral infection. J Biol Chem. 2009 Jan 9;284(2):807-17. PMID:19017631 doi:10.1074/jbc.M804259200
↑ Gao D, Yang YK, Wang RP, Zhou X, Diao FC, Li MD, Zhai ZH, Jiang ZF, Chen DY. REUL is a novel E3 ubiquitin ligase and stimulator of retinoic-acid-inducible gene-I. PLoS One. 2009 Jun 1;4(6):e5760. PMID:19484123 doi:10.1371/journal.pone.0005760
↑ Oshiumi H, Miyashita M, Inoue N, Okabe M, Matsumoto M, Seya T. The ubiquitin ligase Riplet is essential for RIG-I-dependent innate immune responses to RNA virus infection. Cell Host Microbe. 2010 Dec 16;8(6):496-509. PMID:21147464 doi:10.1016/j.chom.2010.11.008
↑ Oshiumi H, Miyashita M, Matsumoto M, Seya T. A distinct role of Riplet-mediated K63-Linked polyubiquitination of the RIG-I repressor domain in human antiviral innate immune responses. PLoS Pathog. 2013;9(8):e1003533. PMID:23950712 doi:10.1371/journal.ppat.1003533
↑ Shi Y, Yuan B, Zhu W, Zhang R, Li L, Hao X, Chen S, Hou F. Ube2D3 and Ube2N are essential for RIG-I-mediated MAVS aggregation in antiviral innate immunity. Nat Commun. 2017 May 4;8:15138. doi: 10.1038/ncomms15138. PMID:28469175 doi:https://dx.doi.org/10.1038/ncomms15138
↑ Cadena C, Ahmad S, Xavier A, Willemsen J, Park S, Park JW, Oh SW, Fujita T, Hou F, Binder M, Hur S. Ubiquitin-Dependent and -Independent Roles of E3 Ligase RIPLET in Innate Immunity. Cell. 2019 May 16;177(5):1187-1200.e16. doi: 10.1016/j.cell.2019.03.017. Epub , 2019 Apr 18. PMID:31006531 doi:https://dx.doi.org/10.1016/j.cell.2019.03.017
↑ Cadena C, Ahmad S, Xavier A, Willemsen J, Park S, Park JW, Oh SW, Fujita T, Hou F, Binder M, Hur S. Ubiquitin-Dependent and -Independent Roles of E3 Ligase RIPLET in Innate Immunity. Cell. 2019 May 16;177(5):1187-1200.e16. doi: 10.1016/j.cell.2019.03.017. Epub , 2019 Apr 18. PMID:31006531 doi:https://dx.doi.org/10.1016/j.cell.2019.03.017

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OCA

[1] Oshiumi H, Matsumoto M, Hatakeyama S, Seya T. Riplet/RNF135, a RING finger protein, ubiquitinates RIG-I to promote interferon-beta induction during the early phase of viral infection. J Biol Chem. 2009 Jan 9;284(2):807-17. PMID:19017631 doi:10.1074/jbc.M804259200

[2] Gao D, Yang YK, Wang RP, Zhou X, Diao FC, Li MD, Zhai ZH, Jiang ZF, Chen DY. REUL is a novel E3 ubiquitin ligase and stimulator of retinoic-acid-inducible gene-I. PLoS One. 2009 Jun 1;4(6):e5760. PMID:19484123 doi:10.1371/journal.pone.0005760

[3] Oshiumi H, Miyashita M, Inoue N, Okabe M, Matsumoto M, Seya T. The ubiquitin ligase Riplet is essential for RIG-I-dependent innate immune responses to RNA virus infection. Cell Host Microbe. 2010 Dec 16;8(6):496-509. PMID:21147464 doi:10.1016/j.chom.2010.11.008

[4] Oshiumi H, Miyashita M, Matsumoto M, Seya T. A distinct role of Riplet-mediated K63-Linked polyubiquitination of the RIG-I repressor domain in human antiviral innate immune responses. PLoS Pathog. 2013;9(8):e1003533. PMID:23950712 doi:10.1371/journal.ppat.1003533

[5] Shi Y, Yuan B, Zhu W, Zhang R, Li L, Hao X, Chen S, Hou F. Ube2D3 and Ube2N are essential for RIG-I-mediated MAVS aggregation in antiviral innate immunity. Nat Commun. 2017 May 4;8:15138. doi: 10.1038/ncomms15138. PMID:28469175 doi:https://dx.doi.org/10.1038/ncomms15138

[6] Cadena C, Ahmad S, Xavier A, Willemsen J, Park S, Park JW, Oh SW, Fujita T, Hou F, Binder M, Hur S. Ubiquitin-Dependent and -Independent Roles of E3 Ligase RIPLET in Innate Immunity. Cell. 2019 May 16;177(5):1187-1200.e16. doi: 10.1016/j.cell.2019.03.017. Epub , 2019 Apr 18. PMID:31006531 doi:https://dx.doi.org/10.1016/j.cell.2019.03.017

[7] Cadena C, Ahmad S, Xavier A, Willemsen J, Park S, Park JW, Oh SW, Fujita T, Hou F, Binder M, Hur S. Ubiquitin-Dependent and -Independent Roles of E3 Ligase RIPLET in Innate Immunity. Cell. 2019 May 16;177(5):1187-1200.e16. doi: 10.1016/j.cell.2019.03.017. Epub , 2019 Apr 18. PMID:31006531 doi:https://dx.doi.org/10.1016/j.cell.2019.03.017

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@@ Line 1: / Line 1: @@
-====
+==Cryo-EM structure of RIG-I:dsRNA filament in complex with RIPLET PrySpry domain (trimer)==
-<StructureSection load='7jl3' size='340' side='right'caption='[[7jl3]]' scene=''>
+<StructureSection load='7jl3' size='340' side='right'caption='[[7jl3]], [[Resolution|resolution]] 4.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7jl3]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JL3 FirstGlance]. <br>
-</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=7jl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jl3 OCA], [https://pdbe.org/7jl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jl3 RCSB], [https://www.ebi.ac.uk/pdbsum/7jl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jl3 ProSAT]</span></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]] 4.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=ALF:TETRAFLUOROALUMINATE+ION'>ALF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7jl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jl3 OCA], [https://pdbe.org/7jl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jl3 RCSB], [https://www.ebi.ac.uk/pdbsum/7jl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jl3 ProSAT]</span></td></tr>
 </table>
+== Disease ==
+[https://www.uniprot.org/uniprot/RN135_HUMAN RN135_HUMAN] Overgrowth-macrocephaly-facial dysmorphism syndrome.
+== Function ==
+[https://www.uniprot.org/uniprot/RN135_HUMAN RN135_HUMAN] E2-dependent E3 ubiquitin-protein ligase that functions as a RIGI coreceptor in the sensing of viral RNAs in cell cytoplasm and the activation of the antiviral innate immune response (PubMed:19017631, PubMed:19484123, PubMed:21147464, PubMed:23950712, PubMed:28469175, PubMed:31006531). Together with the UBE2D3, UBE2N and UB2V1 E2 ligases, catalyzes the 'Lys-63'-linked polyubiquitination of RIGI oligomerized on viral RNAs, an essential step in the activation of the RIG-I signaling pathway (PubMed:19017631, PubMed:21147464, PubMed:28469175, PubMed:31006531). Through a ubiquitin-independent parallel mechanism, which consists in bridging RIGI filaments forming on longer viral RNAs, further activates the RIG-I signaling pathway (PubMed:31006531). This second mechanism that synergizes with the ubiquitin-dependent one would thereby allow an RNA length-dependent regulation of the RIG-I signaling pathway (Probable). Associated with the E2 ligase UBE2N, also constitutively synthesizes unanchored 'Lys-63'-linked polyubiquitin chains that may also activate the RIG-I signaling pathway (PubMed:28469175, PubMed:31006531).<ref>PMID:19017631</ref> <ref>PMID:19484123</ref> <ref>PMID:21147464</ref> <ref>PMID:23950712</ref> <ref>PMID:28469175</ref> <ref>PMID:31006531</ref> <ref>PMID:31006531</ref>
+==See Also==
+*[[Ubiquitin protein ligase 3D structures|Ubiquitin protein ligase 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Z-disk]]
+[[Category: Ahmad S]]
+[[Category: Hur S]]
+[[Category: Kato K]]

7jl3: Difference between revisions

Revision as of 14:52, 6 March 2024

Cryo-EM structure of RIG-I:dsRNA filament in complex with RIPLET PrySpry domain (trimer)

Structural highlights

Disease

Function

See Also

References

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