2qfb

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(New page: 200px<br /><applet load="2qfb" size="350" color="white" frame="true" align="right" spinBox="true" caption="2qfb, resolution 3.0&Aring;" /> '''Crystal structure of ...)
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[[Image:2qfb.jpg|left|200px]]<br /><applet load="2qfb" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2qfb, resolution 3.0&Aring;" />
 
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'''Crystal structure of the regulatory domain of human RIG-I with bound Zn'''<br />
 
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==About this Structure==
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==Crystal structure of the regulatory domain of human RIG-I with bound Zn==
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2QFB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Sites: <scene name='pdbsite=AC1:Zn+Binding+Site+For+Residue+A+1001'>AC1</scene>, <scene name='pdbsite=AC2:Zn+Binding+Site+For+Residue+B+1002'>AC2</scene>, <scene name='pdbsite=AC3:Zn+Binding+Site+For+Residue+C+1003'>AC3</scene>, <scene name='pdbsite=AC4:Zn+Binding+Site+For+Residue+D+1004'>AC4</scene>, <scene name='pdbsite=AC5:Zn+Binding+Site+For+Residue+E+1005'>AC5</scene>, <scene name='pdbsite=AC6:Zn+Binding+Site+For+Residue+F+1006'>AC6</scene>, <scene name='pdbsite=AC7:Zn+Binding+Site+For+Residue+G+1007'>AC7</scene>, <scene name='pdbsite=AC8:Zn+Binding+Site+For+Residue+H+1008'>AC8</scene>, <scene name='pdbsite=AC9:Zn+Binding+Site+For+Residue+I+1009'>AC9</scene> and <scene name='pdbsite=BC1:Zn+Binding+Site+For+Residue+J+1010'>BC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QFB OCA].
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<StructureSection load='2qfb' size='340' side='right'caption='[[2qfb]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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[[Category: Homo sapiens]]
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== Structural highlights ==
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[[Category: Single protein]]
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<table><tr><td colspan='2'>[[2qfb]] is a 10 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=2QFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QFB FirstGlance]. <br>
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[[Category: Cui, S.]]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
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[[Category: ZN]]
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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[[Category: alternative splicing]]
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2qfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qfb OCA], [https://pdbe.org/2qfb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qfb RCSB], [https://www.ebi.ac.uk/pdbsum/2qfb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qfb ProSAT]</span></td></tr>
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[[Category: antiviral defense]]
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</table>
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[[Category: atp-binding]]
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== Disease ==
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[[Category: helicase]]
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[https://www.uniprot.org/uniprot/RIGI_HUMAN RIGI_HUMAN] Singleton-Merten dysplasia. The disease is caused by variants affecting the gene represented in this entry.
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[[Category: hydrolase]]
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== Function ==
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[[Category: immune response]]
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[https://www.uniprot.org/uniprot/RIGI_HUMAN RIGI_HUMAN] Innate immune receptor that senses cytoplasmic viral nucleic acids and activates a downstream signaling cascade leading to the production of type I interferons and pro-inflammatory cytokines (PubMed:15208624, PubMed:15708988, PubMed:16125763, PubMed:16127453, PubMed:16153868, PubMed:17190814, PubMed:18636086, PubMed:19122199, PubMed:19211564, PubMed:24366338, PubMed:28469175, PubMed:29117565, PubMed:31006531, PubMed:34935440, PubMed:35263596, PubMed:36793726). Forms a ribonucleoprotein complex with viral RNAs on which it homooligomerizes to form filaments (PubMed:15208624, PubMed:15708988). The homooligomerization allows the recruitment of RNF135 an E3 ubiquitin-protein ligase that activates and amplifies the RIG-I-mediated antiviral signaling in an RNA length-dependent manner through ubiquitination-dependent and -independent mechanisms (PubMed:28469175, PubMed:31006531). Upon activation, associates with mitochondria antiviral signaling protein (MAVS/IPS1) that activates the IKK-related kinases TBK1 and IKBKE which in turn phosphorylate the interferon regulatory factors IRF3 and IRF7, activating transcription of antiviral immunological genes including the IFN-alpha and IFN-beta interferons (PubMed:28469175, PubMed:31006531). Ligands include 5'-triphosphorylated ssRNAs and dsRNAs but also short dsRNAs (<1 kb in length) (PubMed:15208624, PubMed:15708988, PubMed:19576794, PubMed:19609254, PubMed:21742966). In addition to the 5'-triphosphate moiety, blunt-end base pairing at the 5'-end of the RNA is very essential (PubMed:15208624, PubMed:15708988, PubMed:19576794, PubMed:19609254, PubMed:21742966). Overhangs at the non-triphosphorylated end of the dsRNA RNA have no major impact on its activity (PubMed:15208624, PubMed:15708988, PubMed:19576794, PubMed:19609254, PubMed:21742966). A 3'overhang at the 5'triphosphate end decreases and any 5'overhang at the 5' triphosphate end abolishes its activity (PubMed:15208624, PubMed:15708988, PubMed:19576794, PubMed:19609254, PubMed:21742966). Detects both positive and negative strand RNA viruses including members of the families Paramyxoviridae: Human respiratory syncytial virus and measles virus (MeV), Rhabdoviridae: vesicular stomatitis virus (VSV), Orthomyxoviridae: influenza A and B virus, Flaviviridae: Japanese encephalitis virus (JEV), hepatitis C virus (HCV), dengue virus (DENV) and west Nile virus (WNV) (PubMed:21616437, PubMed:21884169). It also detects rotaviruses and reoviruses (PubMed:21616437, PubMed:21884169). Detects and binds to SARS-CoV-2 RNAs which is inhibited by m6A RNA modifications (Ref.70). Also involved in antiviral signaling in response to viruses containing a dsDNA genome such as Epstein-Barr virus (EBV) (PubMed:19631370). Detects dsRNA produced from non-self dsDNA by RNA polymerase III, such as Epstein-Barr virus-encoded RNAs (EBERs). May play important roles in granulocyte production and differentiation, bacterial phagocytosis and in the regulation of cell migration.<ref>PMID:15208624</ref> <ref>PMID:15708988</ref> <ref>PMID:16125763</ref> <ref>PMID:16127453</ref> <ref>PMID:16153868</ref> <ref>PMID:17190814</ref> <ref>PMID:18636086</ref> <ref>PMID:19122199</ref> <ref>PMID:19211564</ref> <ref>PMID:19576794</ref> <ref>PMID:19609254</ref> <ref>PMID:19631370</ref> <ref>PMID:21742966</ref> <ref>PMID:24366338</ref> <ref>PMID:28469175</ref> <ref>PMID:29117565</ref> <ref>PMID:31006531</ref> <ref>PMID:34935440</ref> <ref>PMID:35263596</ref> <ref>PMID:36793726</ref> [REFERENCE:70]<ref>PMID:21616437</ref> <ref>PMID:21884169</ref>
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[[Category: innate immunity]]
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== Evolutionary Conservation ==
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[[Category: interferon induction]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: nucleotide-binding]]
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Check<jmol>
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[[Category: polymorphism]]
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<jmolCheckbox>
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[[Category: rna-binding]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qf/2qfb_consurf.spt"</scriptWhenChecked>
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[[Category: ubl conjugation]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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[[Category: zinc finger]]
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2qfb ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The ATPase RIG-I senses viral RNAs that contain 5'-triphosphates in the cytoplasm. It initiates a signaling cascade that activates innate immune response by interferon and cytokine production, providing essential antiviral protection for the host. The mode of RNA 5'-triphosphate sensing by RIG-I remains elusive. We show that the C-terminal regulatory domain RD of RIG-I binds viral RNA in a 5'-triphosphate-dependent manner and activates the RIG-I ATPase by RNA-dependent dimerization. The crystal structure of RD reveals a zinc-binding domain that is structurally related to GDP/GTP exchange factors of Rab-like GTPases. The zinc coordination site is essential for RIG-I signaling and is also conserved in MDA5 and LGP2, suggesting related RD domains in all three enzymes. Structure-guided mutagenesis identifies a positively charged groove as likely 5'-triphosphate-binding site of RIG-I. This groove is distinct in MDA5 and LGP2, raising the possibility that RD confers ligand specificity.
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 13 08:20:43 2008''
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The C-terminal regulatory domain is the RNA 5'-triphosphate sensor of RIG-I.,Cui S, Eisenacher K, Kirchhofer A, Brzozka K, Lammens A, Lammens K, Fujita T, Conzelmann KK, Krug A, Hopfner KP Mol Cell. 2008 Feb 1;29(2):169-79. PMID:18243112<ref>PMID:18243112</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2qfb" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Cui S]]
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[[Category: Hopfner KP]]
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[[Category: Lammens A]]
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[[Category: Lammens K]]

Current revision

Crystal structure of the regulatory domain of human RIG-I with bound Zn

PDB ID 2qfb

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