3b6e: Difference between revisions

Latest revision as of 12:27, 21 February 2024

Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domainCrystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain

Structural highlights

3b6e is a 1 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:	X-ray diffraction, Resolution 1.6Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

IFIH1_HUMAN Genetic variation in IFIH1 is associated with diabetes mellitus insulin-dependent type 19 (IDDM19) [MIM:610155. A multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical fetaures are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels.^[1] Note=IFIH1 is the CADM-140 autoantigen, involved in clinically amyopathic dermatomyositis (CADM). This is a chronic inflammatory disorder that shows typical skin manifestations of dermatomyositis but has no or little evidence of clinical myositis. Anti-CADM-140 antibodies appear to be specific to dermatomyositis, especially CADM. Patients with anti-CADM-140 antibodies frequently develop life-threatening acute progressive interstitial lung disease (ILD).^[2] ^[3]

Function

IFIH1_HUMAN Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and proinflammatory cytokines. Its ligands include mRNA lacking 2'-O-methylation at their 5' cap and long-dsRNA (>1 kb in length). Upon ligand binding it associates with mitochondria antiviral signaling protein (MAVS/IPS1) which activates the IKK-related kinases: TBK1 and IKBKE which phosphorylate interferon regulatory factors: IRF3 and IRF7 which in turn activate transcription of antiviral immunological genes, including interferons (IFNs); IFN-alpha and IFN-beta. Responsible for detecting the Picornaviridae family members such as encephalomyocarditis virus (EMCV) and mengo encephalomyocarditis virus (ENMG). Can also detect other viruses such as dengue virus (DENV), west Nile virus (WNV), and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome, such as vaccinia virus. Plays an important role in amplifying innate immune signaling through recognition of RNA metabolites that are produced during virus infection by ribonuclease L (RNase L). May play an important role in enhancing natural killer cell function and may be involved in growth inhibition and apoptosis in several tumor cell lines.^[4] ^[5] ^[6] ^[7] ^[8]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Smyth DJ, Cooper JD, Bailey R, Field S, Burren O, Smink LJ, Guja C, Ionescu-Tirgoviste C, Widmer B, Dunger DB, Savage DA, Walker NM, Clayton DG, Todd JA. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat Genet. 2006 Jun;38(6):617-9. Epub 2006 May 14. PMID:16699517 doi:10.1038/ng1800
↑ Sato S, Hoshino K, Satoh T, Fujita T, Kawakami Y, Fujita T, Kuwana M. RNA helicase encoded by melanoma differentiation-associated gene 5 is a major autoantigen in patients with clinically amyopathic dermatomyositis: Association with rapidly progressive interstitial lung disease. Arthritis Rheum. 2009 Jul;60(7):2193-200. doi: 10.1002/art.24621. PMID:19565506 doi:10.1002/art.24621
↑ Nakashima R, Imura Y, Kobayashi S, Yukawa N, Yoshifuji H, Nojima T, Kawabata D, Ohmura K, Usui T, Fujii T, Okawa K, Mimori T. The RIG-I-like receptor IFIH1/MDA5 is a dermatomyositis-specific autoantigen identified by the anti-CADM-140 antibody. Rheumatology (Oxford). 2010 Mar;49(3):433-40. doi: 10.1093/rheumatology/kep375., Epub 2009 Dec 16. PMID:20015976 doi:10.1093/rheumatology/kep375
↑ Cocude C, Truong MJ, Billaut-Mulot O, Delsart V, Darcissac E, Capron A, Mouton Y, Bahr GM. A novel cellular RNA helicase, RH116, differentially regulates cell growth, programmed cell death and human immunodeficiency virus type 1 replication. J Gen Virol. 2003 Dec;84(Pt 12):3215-25. PMID:14645903
↑ Bamming D, Horvath CM. Regulation of signal transduction by enzymatically inactive antiviral RNA helicase proteins MDA5, RIG-I, and LGP2. J Biol Chem. 2009 Apr 10;284(15):9700-12. doi: 10.1074/jbc.M807365200. Epub 2009 , Feb 11. PMID:19211564 doi:10.1074/jbc.M807365200
↑ Pichlmair A, Schulz O, Tan CP, Rehwinkel J, Kato H, Takeuchi O, Akira S, Way M, Schiavo G, Reis e Sousa C. Activation of MDA5 requires higher-order RNA structures generated during virus infection. J Virol. 2009 Oct;83(20):10761-9. doi: 10.1128/JVI.00770-09. Epub 2009 Aug 5. PMID:19656871 doi:10.1128/JVI.00770-09
↑ Jiang M, Osterlund P, Sarin LP, Poranen MM, Bamford DH, Guo D, Julkunen I. Innate immune responses in human monocyte-derived dendritic cells are highly dependent on the size and the 5' phosphorylation of RNA molecules. J Immunol. 2011 Aug 15;187(4):1713-21. doi: 10.4049/jimmunol.1100361. Epub 2011, Jul 8. PMID:21742966 doi:10.4049/jimmunol.1100361
↑ Zust R, Cervantes-Barragan L, Habjan M, Maier R, Neuman BW, Ziebuhr J, Szretter KJ, Baker SC, Barchet W, Diamond MS, Siddell SG, Ludewig B, Thiel V. Ribose 2'-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5. Nat Immunol. 2011 Feb;12(2):137-43. doi: 10.1038/ni.1979. Epub 2011 Jan 9. PMID:21217758 doi:10.1038/ni.1979

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Smyth DJ, Cooper JD, Bailey R, Field S, Burren O, Smink LJ, Guja C, Ionescu-Tirgoviste C, Widmer B, Dunger DB, Savage DA, Walker NM, Clayton DG, Todd JA. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat Genet. 2006 Jun;38(6):617-9. Epub 2006 May 14. PMID:16699517 doi:10.1038/ng1800

[2] Sato S, Hoshino K, Satoh T, Fujita T, Kawakami Y, Fujita T, Kuwana M. RNA helicase encoded by melanoma differentiation-associated gene 5 is a major autoantigen in patients with clinically amyopathic dermatomyositis: Association with rapidly progressive interstitial lung disease. Arthritis Rheum. 2009 Jul;60(7):2193-200. doi: 10.1002/art.24621. PMID:19565506 doi:10.1002/art.24621

[3] Nakashima R, Imura Y, Kobayashi S, Yukawa N, Yoshifuji H, Nojima T, Kawabata D, Ohmura K, Usui T, Fujii T, Okawa K, Mimori T. The RIG-I-like receptor IFIH1/MDA5 is a dermatomyositis-specific autoantigen identified by the anti-CADM-140 antibody. Rheumatology (Oxford). 2010 Mar;49(3):433-40. doi: 10.1093/rheumatology/kep375., Epub 2009 Dec 16. PMID:20015976 doi:10.1093/rheumatology/kep375

[4] Cocude C, Truong MJ, Billaut-Mulot O, Delsart V, Darcissac E, Capron A, Mouton Y, Bahr GM. A novel cellular RNA helicase, RH116, differentially regulates cell growth, programmed cell death and human immunodeficiency virus type 1 replication. J Gen Virol. 2003 Dec;84(Pt 12):3215-25. PMID:14645903

[5] Bamming D, Horvath CM. Regulation of signal transduction by enzymatically inactive antiviral RNA helicase proteins MDA5, RIG-I, and LGP2. J Biol Chem. 2009 Apr 10;284(15):9700-12. doi: 10.1074/jbc.M807365200. Epub 2009 , Feb 11. PMID:19211564 doi:10.1074/jbc.M807365200

[6] Pichlmair A, Schulz O, Tan CP, Rehwinkel J, Kato H, Takeuchi O, Akira S, Way M, Schiavo G, Reis e Sousa C. Activation of MDA5 requires higher-order RNA structures generated during virus infection. J Virol. 2009 Oct;83(20):10761-9. doi: 10.1128/JVI.00770-09. Epub 2009 Aug 5. PMID:19656871 doi:10.1128/JVI.00770-09

[7] Jiang M, Osterlund P, Sarin LP, Poranen MM, Bamford DH, Guo D, Julkunen I. Innate immune responses in human monocyte-derived dendritic cells are highly dependent on the size and the 5' phosphorylation of RNA molecules. J Immunol. 2011 Aug 15;187(4):1713-21. doi: 10.4049/jimmunol.1100361. Epub 2011, Jul 8. PMID:21742966 doi:10.4049/jimmunol.1100361

[8] Zust R, Cervantes-Barragan L, Habjan M, Maier R, Neuman BW, Ziebuhr J, Szretter KJ, Baker SC, Barchet W, Diamond MS, Siddell SG, Ludewig B, Thiel V. Ribose 2'-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5. Nat Immunol. 2011 Feb;12(2):137-43. doi: 10.1038/ni.1979. Epub 2011 Jan 9. PMID:21217758 doi:10.1038/ni.1979

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[2]

[3]

[4]

[5]

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@@ Line 1: / Line 1: @@
-[[Image:3b6e.gif|left|200px]]<br /><applet load="3b6e" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="3b6e, resolution 1.60&Aring;" />
-'''Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain'''<br />
-==Disease==
+==Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain==
-Known diseases associated with this structure: Diabetes mellitus, insulin-dependent, susceptibility to OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=606951 606951]]
+<StructureSection load='3b6e' size='340' side='right'caption='[[3b6e]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[3b6e]] is a 1 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=3B6E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B6E FirstGlance]. <br>
-B6E 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=NA:'>NA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B6E OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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=3b6e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b6e OCA], [https://pdbe.org/3b6e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b6e RCSB], [https://www.ebi.ac.uk/pdbsum/3b6e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b6e ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/IFIH1_HUMAN IFIH1_HUMAN] Genetic variation in IFIH1 is associated with diabetes mellitus insulin-dependent type 19 (IDDM19) [MIM:[https://omim.org/entry/610155 610155]. A multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical fetaures are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels.<ref>PMID:16699517</ref>   Note=IFIH1 is the CADM-140 autoantigen, involved in clinically amyopathic dermatomyositis (CADM). This is a chronic inflammatory disorder that shows typical skin manifestations of dermatomyositis but has no or little evidence of clinical myositis. Anti-CADM-140 antibodies appear to be specific to dermatomyositis, especially CADM. Patients with anti-CADM-140 antibodies frequently develop life-threatening acute progressive interstitial lung disease (ILD).<ref>PMID:19565506</ref> <ref>PMID:20015976</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/IFIH1_HUMAN IFIH1_HUMAN] Innate immune receptor which acts as a cytoplasmic sensor of viral nucleic acids and plays a major role in sensing viral infection and in the activation of a cascade of antiviral responses including the induction of type I interferons and proinflammatory cytokines. Its ligands include mRNA lacking 2'-O-methylation at their 5' cap and long-dsRNA (>1 kb in length). Upon ligand binding it associates with mitochondria antiviral signaling protein (MAVS/IPS1) which activates the IKK-related kinases: TBK1 and IKBKE which phosphorylate interferon regulatory factors: IRF3 and IRF7 which in turn activate transcription of antiviral immunological genes, including interferons (IFNs); IFN-alpha and IFN-beta. Responsible for detecting the Picornaviridae family members such as encephalomyocarditis virus (EMCV) and mengo encephalomyocarditis virus (ENMG). Can also detect other viruses such as dengue virus (DENV), west Nile virus (WNV), and reovirus. Also involved in antiviral signaling in response to viruses containing a dsDNA genome, such as vaccinia virus. Plays an important role in amplifying innate immune signaling through recognition of RNA metabolites that are produced during virus infection by ribonuclease L (RNase L). May play an important role in enhancing natural killer cell function and may be involved in growth inhibition and apoptosis in several tumor cell lines.<ref>PMID:14645903</ref> <ref>PMID:19211564</ref> <ref>PMID:19656871</ref> <ref>PMID:21742966</ref> <ref>PMID:21217758</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b6/3b6e_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=3b6e ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Arrowsmith, C H.]]
+[[Category: Arrowsmith CH]]
-[[Category: Berg, S Van Den.]]
+[[Category: Berglund H]]
-[[Category: Berglund, H.]]
+[[Category: Busam RD]]
-[[Category: Busam, R D.]]
+[[Category: Collins R]]
-[[Category: Collins, R.]]
+[[Category: Dahlgren LG]]
-[[Category: Dahlgren, L G.]]
+[[Category: Edwards AM]]
-[[Category: Edwards, A M.]]
+[[Category: Flodin S]]
-[[Category: Flodin, S.]]
+[[Category: Flores A]]
-[[Category: Flores, A.]]
+[[Category: Graslund S]]
-[[Category: Graslund, S.]]
+[[Category: Hammarstrom M]]
-[[Category: Hammarstrom, M.]]
+[[Category: Holmberg-Schiavone L]]
-[[Category: Holmberg-Schiavone, L.]]
+[[Category: Johansson I]]
-[[Category: Johansson, I.]]
+[[Category: Kallas A]]
-[[Category: Kallas, A.]]
+[[Category: Karlberg T]]
-[[Category: Karlberg, T.]]
+[[Category: Kotenyova T]]
-[[Category: Kotenyova, T.]]
+[[Category: Lehtio L]]
-[[Category: Lehtio, L.]]
+[[Category: Moche M]]
-[[Category: Moche, M.]]
+[[Category: Nilsson ME]]
-[[Category: Nilsson, M E.]]
+[[Category: Nordlund P]]
-[[Category: Nordlund, P.]]
+[[Category: Nyman T]]
-[[Category: Nyman, T.]]
+[[Category: Persson C]]
-[[Category: Persson, C.]]
+[[Category: Sagemark J]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: Svensson L]]
-[[Category: Sagemark, J.]]
+[[Category: Thorsell AG]]
-[[Category: Svensson, L.]]
+[[Category: Tresaugues L]]
-[[Category: Thorsell, A G.]]
+[[Category: Van Den Berg S]]
-[[Category: Tresaugues, L.]]
+[[Category: Weigelt J]]
-[[Category: Weigelt, J.]]
+[[Category: Welin M]]
-[[Category: Welin, M.]]
-[[Category: NA]]
-[[Category: alternative splicing]]
-[[Category: antiviral defense]]
-[[Category: atp-binding]]
-[[Category: cytoplasm]]
-[[Category: dech]]
-[[Category: dexd/h rna-binding helicase]]
-[[Category: diabetes mellitus]]
-[[Category: host-virus interaction]]
-[[Category: hydrolase]]
-[[Category: ifih1]]
-[[Category: immune response]]
-[[Category: innate immunity]]
-[[Category: nucleotide-binding]]
-[[Category: nucleus]]
-[[Category: phosphorylation]]
-[[Category: polymorphism]]
-[[Category: sgc]]
-[[Category: structural genomics]]
-[[Category: structural genomics consortium]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:03:35 2008''

3b6e: Difference between revisions

Latest revision as of 12:27, 21 February 2024

Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domainCrystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain

Structural highlights

Disease

Function

Evolutionary Conservation

References

Contents

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3b6e: Difference between revisions

Latest revision as of 12:27, 21 February 2024

Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domainCrystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain

Structural highlights

Disease

Function

Evolutionary Conservation

References

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Navigation menu

Search