+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29823 | |||||||||
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Title | Cryo-EM structure of RNP end | |||||||||
Map data | Cryo-EM structure of RNP end | |||||||||
Sample |
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Keywords | ribonucleoprotein complex / RNA sensor / RIG-I like receptor / Ubiquitination / E3 ligase / TRIM family / ANTIVIRAL PROTEIN / Transferase-Hydrolase-RNA complex | |||||||||
Function / homology | Function and homology information RIG-I binding / free ubiquitin chain polymerization / regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production ...RIG-I binding / free ubiquitin chain polymerization / regulation of type III interferon production / RIG-I signaling pathway / positive regulation of myeloid dendritic cell cytokine production / OAS antiviral response / detection of virus / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / positive regulation of response to cytokine stimulus / positive regulation of granulocyte macrophage colony-stimulating factor production / pattern recognition receptor activity / TRAF6 mediated IRF7 activation / regulation of innate immune response / response to exogenous dsRNA / cellular response to exogenous dsRNA / cytoplasmic pattern recognition receptor signaling pathway / protein K63-linked ubiquitination / positive regulation of interferon-alpha production / antiviral innate immune response / TRAF6 mediated NF-kB activation / bicellular tight junction / ribonucleoprotein complex binding / regulation of cell migration / positive regulation of defense response to virus by host / positive regulation of interferon-beta production / Negative regulators of DDX58/IFIH1 signaling / positive regulation of interleukin-8 production / response to virus / RING-type E3 ubiquitin transferase / DDX58/IFIH1-mediated induction of interferon-alpha/beta / protein homooligomerization / ISG15 antiviral mechanism / ruffle membrane / cytoplasmic stress granule / protein polyubiquitination / positive regulation of interleukin-6 production / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / positive regulation of DNA-binding transcription factor activity / Ovarian tumor domain proteases / actin cytoskeleton / double-stranded RNA binding / positive regulation of tumor necrosis factor production / TRAF3-dependent IRF activation pathway / gene expression / double-stranded DNA binding / defense response to virus / RNA helicase activity / single-stranded RNA binding / protein ubiquitination / RNA helicase / Ub-specific processing proteases / ribonucleoprotein complex / innate immune response / ubiquitin protein ligase binding / GTP binding / positive regulation of gene expression / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / ATP binding / identical protein binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Wang W / Pyle AM | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Riplet:RIG-I:dsRNA complex (end-inter) Authors: Wang W / Pyle AM | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29823.map.gz | 65.4 MB | EMDB map data format | |
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Header (meta data) | emd-29823-v30.xml emd-29823.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29823_fsc.xml | 9.4 KB | Display | FSC data file |
Images | emd_29823.png | 96.8 KB | ||
Masks | emd_29823_msk_1.map | 70.2 MB | Mask map | |
Filedesc metadata | emd-29823.cif.gz | 6.7 KB | ||
Others | emd_29823_half_map_1.map.gz emd_29823_half_map_2.map.gz | 54.6 MB 54.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29823 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29823 | HTTPS FTP |
-Related structure data
Related structure data | 8g7tMC 8g7uC 8g7vC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29823.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of RNP end | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.839 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29823_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half Map 1
File | emd_29823_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_29823_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of RNP end
Entire | Name: Complex of RNP end |
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Components |
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-Supramolecule #1: Complex of RNP end
Supramolecule | Name: Complex of RNP end / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Antiviral innate immune response receptor RIG-I
Macromolecule | Name: Antiviral innate immune response receptor RIG-I / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RNA helicase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 106.740555 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTTEQRRSLQ AFQDYIRKTL DPTYILSYMA PWFREEEVQY IQAEKNNKGP MEAATLFLKF LLELQEEGWF RGFLDALDHA GYSGLYEAI ESWDFKKIEK LEEYRLLLKR LQPEFKTRII PTDIISDLSE CLINQECEEI LQICSTKGMM AGAEKLVECL L RSDKENWP ...String: MTTEQRRSLQ AFQDYIRKTL DPTYILSYMA PWFREEEVQY IQAEKNNKGP MEAATLFLKF LLELQEEGWF RGFLDALDHA GYSGLYEAI ESWDFKKIEK LEEYRLLLKR LQPEFKTRII PTDIISDLSE CLINQECEEI LQICSTKGMM AGAEKLVECL L RSDKENWP KTLKLALEKE RNKFSELWIV EKGIKDVETE DLEDKMETSD IQIFYQEDPE CQNLSENSCP PSEVSDTNLY SP FKPRNYQ LELALPAMKG KNTIICAPTG CGKTFVSLLI CEHHLKKFPQ GQKGKVVFFA NQIPVYEQQK SVFSKYFERH GYR VTGISG ATAENVPVEQ IVENNDIIIL TPQILVNNLK KGTIPSLSIF TLMIFDECHN TSKQHPYNMI MFNYLDQKLG GSSG PLPQV IGLTASVGVG DAKNTDEALD YICKLCASLD ASVIATVKHN LEELEQVVYK PQKFFRKVES RISDKFKYII AQLMR DTES LAKRICKDLE NLSQIQNREF GTQKYEQWIV TVQKACMVFQ MPDKDEESRI CKALFLYTSH LRKYNDALII SEHARM KDA LDYLKDFFSN VRAAGFDEIE QDLTQRFEEK LQELESVSRD PSNENPKLED LCFILQEEYH LNPETITILF VKTRALV DA LKNWIEGNPK LSFLKPGILT GRGKTNQNTG MTLPAQKCIL DAFKASGDHN ILIATSVADE GIDIAQCNLV ILYEYVGN V IKMIQTRGRG RARGSKCFLL TSNAGVIEKE QINMYKEKMM NDSILRLQTW DEAVFREKIL HIQTHEKFIR DSQEKPKPV PDKENKKLLC RKCKALACYT ADVRVIEECH YTVLGDAFKE CFVSRPHPKP KQFSSFEKRA KIFCARQNCS HDWGIHVKYK TFEIPVIKI ESFVVEDIAT GVQTLYSKWK DFHFEKIPFD PAEMSK UniProtKB: Antiviral innate immune response receptor RIG-I |
-Macromolecule #2: E3 ubiquitin-protein ligase RNF135
Macromolecule | Name: E3 ubiquitin-protein ligase RNF135 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 47.946305 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAGLGLGSAV PVWLAEDDLG CIICQGLLDW PATLPCGHSF CRHCLEALWG ARDARRWACP TCRQGAAQQP HLRKNTLLQD LADKYRRAA REIQAGSDPA HCPCPGSSSL SSAAARPRRR PELQRVAVEK SITEVAQELT ELVEHLVDIV RSLQNQRPLS E SGPDNELS ...String: MAGLGLGSAV PVWLAEDDLG CIICQGLLDW PATLPCGHSF CRHCLEALWG ARDARRWACP TCRQGAAQQP HLRKNTLLQD LADKYRRAA REIQAGSDPA HCPCPGSSSL SSAAARPRRR PELQRVAVEK SITEVAQELT ELVEHLVDIV RSLQNQRPLS E SGPDNELS ILGKAFSSGV DLSMASPKLV TSDTAAGKIR DILHDLEEIQ EKLQESVTWK EAPEAQMQGE LLEAPSSSSC PL PDQSHPA LRRASRFAQW AIHPTFNLKS LSCSLEVSKD SRTVTVSHRP QPYRWSCERF STSQVLCSQA LSSGKHYWEV DTR NCSHWA VGVASWEMSR DQVLGRTMDS CCVEWKGTSQ LSAWHMVKET VLGSDRPGVV GIWLNLEEGK LAFYSVDNQE KLLY ECTIS ASSPLYPAFW LYGLHPGNYL IIKQVKV UniProtKB: E3 ubiquitin-protein ligase RNF135 |
-Macromolecule #3: p3dsRNA24a
Macromolecule | Name: p3dsRNA24a / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 7.885581 KDa |
Sequence | String: (GTP)GACGUACGU UUCGCGACUG UAGA |
-Macromolecule #4: p3dsRNA24b
Macromolecule | Name: p3dsRNA24b / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 7.788551 KDa |
Sequence | String: (UTP)CUACAGUCG CGAAACGUAC GUCC |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |