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Yorodumi- EMDB-16891: Structure of the UBE1L activating enzyme bound to ISG15 and UBE2L6 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16891 | |||||||||||||||
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Title | Structure of the UBE1L activating enzyme bound to ISG15 and UBE2L6 | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | ubiquitin-like / ISG15 / interferon-stimulated genes / antiviral / ANTIVIRAL PROTEIN | |||||||||||||||
Function / homology | Function and homology information ISG15 activating enzyme activity / ISG15 transferase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / protein localization to mitochondrion / NS1 Mediated Effects on Host Pathways / response to type I interferon / RSV-host interactions ...ISG15 activating enzyme activity / ISG15 transferase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / protein localization to mitochondrion / NS1 Mediated Effects on Host Pathways / response to type I interferon / RSV-host interactions / negative regulation of type I interferon-mediated signaling pathway / E2 ubiquitin-conjugating enzyme / negative regulation of viral genome replication / ubiquitin conjugating enzyme activity / positive regulation of interleukin-10 production / polyubiquitin modification-dependent protein binding / positive regulation of bone mineralization / ubiquitin ligase complex / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / ubiquitin binding / integrin-mediated signaling pathway / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / protein modification process / PKR-mediated signaling / ISG15 antiviral mechanism / modification-dependent protein catabolic process / protein polyubiquitination / protein tag activity / ubiquitin-protein transferase activity / positive regulation of type II interferon production / Interferon alpha/beta signaling / Antigen processing: Ubiquitination & Proteasome degradation / integrin binding / ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / defense response to bacterium / Amyloid fiber formation / innate immune response / DNA damage response / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Wallace I / Kheewoong B / Prabu JR / Vollrath R / von Gronau S / Schulman BA / Swatek KN | |||||||||||||||
Funding support | United Kingdom, Germany, European Union, 4 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Insights into the ISG15 transfer cascade by the UBE1L activating enzyme. Authors: Iona Wallace / Kheewoong Baek / J Rajan Prabu / Ronnald Vollrath / Susanne von Gronau / Brenda A Schulman / Kirby N Swatek / Abstract: The attachment of the ubiquitin-like protein ISG15 to substrates by specific E1-E2-E3 enzymes is a well-established signalling mechanism of the innate immune response. Here, we present a 3.45 Å ...The attachment of the ubiquitin-like protein ISG15 to substrates by specific E1-E2-E3 enzymes is a well-established signalling mechanism of the innate immune response. Here, we present a 3.45 Å cryo-EM structure of a chemically trapped UBE1L-UBE2L6 complex bound to activated ISG15. This structure reveals the details of the first steps of ISG15 recognition and UBE2L6 recruitment by UBE1L (also known as UBA7). Taking advantage of viral effector proteins from severe acute respiratory coronavirus 2 (SARS-CoV-2) and influenza B virus (IBV), we validate the structure and confirm the importance of the ISG15 C-terminal ubiquitin-like domain in the adenylation reaction. Moreover, biochemical characterization of the UBE1L-ISG15 and UBE1L-UBE2L6 interactions enables the design of ISG15 and UBE2L6 mutants with altered selectively for the ISG15 and ubiquitin conjugation pathways. Together, our study helps to define the molecular basis of these interactions and the specificity determinants that ensure the fidelity of ISG15 signalling during the antiviral response. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16891.map.gz | 8.3 MB | EMDB map data format | |
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Header (meta data) | emd-16891-v30.xml emd-16891.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16891_fsc.xml | 10.3 KB | Display | FSC data file |
Images | emd_16891.png | 114.5 KB | ||
Masks | emd_16891_msk_1.map | 91.1 MB | Mask map | |
Filedesc metadata | emd-16891.cif.gz | 6.6 KB | ||
Others | emd_16891_additional_1.map.gz emd_16891_half_map_1.map.gz emd_16891_half_map_2.map.gz | 81.1 MB 71.4 MB 71.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16891 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16891 | HTTPS FTP |
-Related structure data
Related structure data | 8oifMC 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_16891.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8512 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16891_msk_1.map | ||||||||||||
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-Additional map: #1
File | emd_16891_additional_1.map | ||||||||||||
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-Half map: #2
File | emd_16891_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_16891_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex consisting of UBE1L, UBE2L6, and full-length ISG15.
Entire | Name: Ternary complex consisting of UBE1L, UBE2L6, and full-length ISG15. |
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Components |
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-Supramolecule #1: Ternary complex consisting of UBE1L, UBE2L6, and full-length ISG15.
Supramolecule | Name: Ternary complex consisting of UBE1L, UBE2L6, and full-length ISG15. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: UBE2L6
Supramolecule | Name: UBE2L6 / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: ISG15
Supramolecule | Name: ISG15 / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Ubiquitin-like modifier-activating enzyme 7
Macromolecule | Name: Ubiquitin-like modifier-activating enzyme 7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 111.966234 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GSMDALDASK LLDEELYSRQ LYVLGSPAMQ RIQGARVLVS GLQGLGAEVA KNLVLMGVGS LTLHDPHPTC WSDLAAQFLL SEQDLERSR AEASQELLAQ LNRAVQVVVH TGDITEDLLL DFQVVVLTAA KLEEQLKVGT LCHKHGVCFL AADTRGLVGQ L FCDFGEDF ...String: GSMDALDASK LLDEELYSRQ LYVLGSPAMQ RIQGARVLVS GLQGLGAEVA KNLVLMGVGS LTLHDPHPTC WSDLAAQFLL SEQDLERSR AEASQELLAQ LNRAVQVVVH TGDITEDLLL DFQVVVLTAA KLEEQLKVGT LCHKHGVCFL AADTRGLVGQ L FCDFGEDF TVQDPTEAEP LTAAIQHISQ GSPGILTLRK GANTHYFRDG DLVTFSGIEG MVELNDCDPR SIHVREDGSL EI GDTTTFS RYLRGGAITE VKRPKTVRHK SLDTALLQPH VVAQSSQEVH HAHCLHQAFC ALHKFQHLHG RPPQPWDPVD AET VVGLAR DLEPLKRTEE EPLEEPLDEA LVRTVALSSA GVLSPMVAML GAVAAQEVLK AISRKFMPLD QWLYFDALDC LPED GELLP SPEDCALRGS RYDGQIAVFG AGFQEKLRRQ HYLLVGAGAI GCELLKVFAL VGLGAGNSGG LTVVDMDHIE RSNLS RQFL FRSQDVGRPK AEVAAAAARG LNPDLQVIPL TYPLDPTTEH IYGDNFFSRV DGVAAALDSF QARRYVAARC THYLKP LLE AGTSGTWGSA TVFMPHVTEA YRAPASAAAS EDAPYPVCTV RYFPSTAEHT LQWARHEFEE LFRLSAETIN HHQQAHT SL ADMDEPQTLT LLKPVLGVLR VRPQNWQDCV AWALGHWKLC FHYGIKQLLR HFPPNKVLED GTPFWSGPKQ CPQPLEFD T NQDTHLLYVL AAANLYAQMH GLPGSQDWTA LRELLKLLPQ PDPQQMAPIF ASNLELASAS AEFGPEQQKE LNKALEVWS VGPPLKPLMF EKDDDSNFHV DFVVAAASLR CQNYGIPPVN RAQSKRIVGQ IIPAIATTTA AVAGLLGLEL YKVVSGPRPR SAFRHSYLH LAENYLIRYM PFAPAIQTFH HLKWTSWDRL KVPAGQPERT LESLLAHLQE QHGLRVRILL HGSALLYAAG W SPEKQAQH LPLRVTELVQ QLTGQAPAPG QRVLVLELSC EGDDEDTAFP PLHYEL UniProtKB: Ubiquitin-like modifier-activating enzyme 7 |
-Macromolecule #2: Ubiquitin-like protein ISG15
Macromolecule | Name: Ubiquitin-like protein ISG15 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 17.147637 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGWDLTVKML AGNEFQVSLS SSMSVSELKA QITQKIGVHA FQQRLAVHPS GVALQDRVPL ASQGLGPGST VLLVVDKSDE PLSILVRNN KGRSSTYEVR LTQTVAHLKQ QVSGLEGVQD DLFWLTFEGK PLEDQLPLGE YGLKPLSTVF MNLRLRGG UniProtKB: Ubiquitin-like protein ISG15 |
-Macromolecule #3: Ubiquitin/ISG15-conjugating enzyme E2 L6
Macromolecule | Name: Ubiquitin/ISG15-conjugating enzyme E2 L6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 17.912719 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPMMASMRVV KELEDLQKKP PPYLRNLSSD DANVLVWHAL LLPDQPPYHL KAFNLRISFP PEYPFKPPMI KFTTKIYHPN VDENGQICL PIISSENWKP STKTSQVLEA LNVLVNRPNI REPLRMDLAD LLTQNPELFR KNAEEFTLRF GVDRPS UniProtKB: Ubiquitin/ISG15-conjugating enzyme E2 L6 |
-Macromolecule #4: ADENOSINE MONOPHOSPHATE
Macromolecule | Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: AMP |
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Molecular weight | Theoretical: 347.221 Da |
Chemical component information | ChemComp-AMP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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: 3.0 µm / Nominal defocus min: 1.2 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 |