+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26066 | |||||||||
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Title | Structure of Enterobacter cloacae Cap2-CdnD02 2:1 complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CBASS / ubiquitin E1/E2 / bacterial anti-phage defense / cGAS / TRANSFERASE | |||||||||
Function / homology | Function and homology information nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / GTP binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Enterobacter cloacae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Gu Y / Ye Q | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nature / Year: 2023 Title: An E1-E2 fusion protein primes antiviral immune signalling in bacteria. Authors: Hannah E Ledvina / Qiaozhen Ye / Yajie Gu / Ashley E Sullivan / Yun Quan / Rebecca K Lau / Huilin Zhou / Kevin D Corbett / Aaron T Whiteley / Abstract: In all organisms, innate immune pathways sense infection and rapidly activate potent immune responses while avoiding inappropriate activation (autoimmunity). In humans, the innate immune receptor ...In all organisms, innate immune pathways sense infection and rapidly activate potent immune responses while avoiding inappropriate activation (autoimmunity). In humans, the innate immune receptor cyclic GMP-AMP synthase (cGAS) detects viral infection to produce the nucleotide second messenger cyclic GMP-AMP (cGAMP), which initiates stimulator of interferon genes (STING)-dependent antiviral signalling. Bacteria encode evolutionary predecessors of cGAS called cGAS/DncV-like nucleotidyltransferases (CD-NTases), which detect bacteriophage infection and produce diverse nucleotide second messengers. How bacterial CD-NTase activation is controlled remains unknown. Here we show that CD-NTase-associated protein 2 (Cap2) primes bacterial CD-NTases for activation through a ubiquitin transferase-like mechanism. A cryo-electron microscopy structure of the Cap2-CD-NTase complex reveals Cap2 as an all-in-one ubiquitin transferase-like protein, with distinct domains resembling eukaryotic E1 and E2 proteins. The structure captures a reactive-intermediate state with the CD-NTase C terminus positioned in the Cap2 E1 active site and conjugated to AMP. Cap2 conjugates the CD-NTase C terminus to a target molecule that primes the CD-NTase for increased cGAMP production. We further demonstrate that a specific endopeptidase, Cap3, balances Cap2 activity by cleaving CD-NTase-target conjugates. Our data demonstrate that bacteria control immune signalling using an ancient, minimized ubiquitin transferase-like system and provide insight into the evolution of the E1 and E2 machinery across domains of life. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26066.map.gz | 162.8 MB | EMDB map data format | |
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Header (meta data) | emd-26066-v30.xml emd-26066.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26066_fsc.xml | 15.2 KB | Display | FSC data file |
Images | emd_26066.png | 135 KB | ||
Filedesc metadata | emd-26066.cif.gz | 6.4 KB | ||
Others | emd_26066_half_map_1.map.gz emd_26066_half_map_2.map.gz | 301.9 MB 301.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26066 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26066 | HTTPS FTP |
-Validation report
Summary document | emd_26066_validation.pdf.gz | 913.1 KB | Display | EMDB validaton report |
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Full document | emd_26066_full_validation.pdf.gz | 912.7 KB | Display | |
Data in XML | emd_26066_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | emd_26066_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26066 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26066 | HTTPS FTP |
-Related structure data
Related structure data | 7tqdMC 7to3C 7tsqC 7tsxC 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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-Map
File | Download / File: emd_26066.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_26066_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26066_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of Cap2 and CdnD02 in a 2:1 stoichiometry.
Entire | Name: Ternary complex of Cap2 and CdnD02 in a 2:1 stoichiometry. |
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Components |
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-Supramolecule #1: Ternary complex of Cap2 and CdnD02 in a 2:1 stoichiometry.
Supramolecule | Name: Ternary complex of Cap2 and CdnD02 in a 2:1 stoichiometry. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Enterobacter cloacae (bacteria) |
Molecular weight | Theoretical: 179.4 KDa |
-Macromolecule #1: Cap2
Macromolecule | Name: Cap2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Enterobacter cloacae (bacteria) |
Molecular weight | Theoretical: 67.024953 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSTVVQQVPA ELQAALTLIN NDPRMRTNNA WALSADKRWS LKFTAELSVP CSSFMPDNSV WHLVLWQEET LIRIEVYPDK SEGISATFQ HQNYNFSDAS TREWTSGNPA LENTPTVFGR NLWGLEPEAL LDRISWRLSR LLLWIDAAAQ EKLATTGDAV E LPAFPDQS ...String: MSTVVQQVPA ELQAALTLIN NDPRMRTNNA WALSADKRWS LKFTAELSVP CSSFMPDNSV WHLVLWQEET LIRIEVYPDK SEGISATFQ HQNYNFSDAS TREWTSGNPA LENTPTVFGR NLWGLEPEAL LDRISWRLSR LLLWIDAAAQ EKLATTGDAV E LPAFPDQS PFTVIGFSEQ IDDLPFWASK TGEWGFASST GLPGAHGTLF LREFLDNKGK LIRTTKWSPF MRKGARTTNA VW SVLPTLP VLAPWQAPRT WQELSHCFAQ CGLSLPDLFS DIGRSVRALR KQRAPGLLLL GFPLENKIGD EPARIHWLAL RLA GLSNTM TKRPGFRPTE RNRRTWDREQ PLSQEPIRWV RTQNWAADQL RTRGEAANDI RSKKVLIIGA GSLGSMIAEN LMRI GVVSQ GILDADLLQT GNLSRHALTM TSVGHNKAAA LVEHLNRILP DASARSFSCA FPPESEVAKN SLRQYDVIID CTGDD GVLK SLAAFDWKSE KIFISLAMTW RAEGLFAFAA SETSFPVTDA SSRFNASASP EIDMDEARIE GIGAWHPVFP ARADDV QLW AAVGTKFICR VVSAPGRIYE YFKQMPDGTV EKEPHEY |
-Macromolecule #2: Cyclic AMP-AMP-GMP synthase
Macromolecule | Name: Cyclic AMP-AMP-GMP synthase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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Source (natural) | Organism: Enterobacter cloacae (bacteria) |
Molecular weight | Theoretical: 45.506828 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKSSHHHHHH ENLYFQSNAE LQPQFNEFLA NIRPTDTQKE DWKSGARTLR ERLKNFEPLK EIVVSTFLQG SIRRSTAIRP LGDKRPDVD IVVVTNLDHT RMSPTDAMDL FIPFLEKYYP GKWETQGRSF GITLSYVELD LVITAIPESG AEKSHLEQLY K SESVLTVN ...String: MKSSHHHHHH ENLYFQSNAE LQPQFNEFLA NIRPTDTQKE DWKSGARTLR ERLKNFEPLK EIVVSTFLQG SIRRSTAIRP LGDKRPDVD IVVVTNLDHT RMSPTDAMDL FIPFLEKYYP GKWETQGRSF GITLSYVELD LVITAIPESG AEKSHLEQLY K SESVLTVN SLEEQTDWRL NKSWTPNTGW LSESNSAQVE DAPASEWKAH PLVLPDREKN EWGRTHPLAQ IRWTAEKNRL CN GHYINLV RAVKWWRQQN SEDLPKYPKG YPLEHLIGNA LDNGTTSMAQ GLVQLMDTFL SRWAAIYNQK SKPWLSDHGV AEH DVMARL TAEDFCSFYE GIASAAEIAR NALASEEPQE SAQLWRQLFG SKFPLPGPQG GDRNGGFTTP SKPAEPQKTG RFA UniProtKB: Cyclic AMP-AMP-GMP synthase |
-Macromolecule #3: ADENOSINE MONOPHOSPHATE
Macromolecule | Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: AMP |
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Molecular weight | Theoretical: 347.221 Da |
Chemical component information | ChemComp-AMP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.9 mg/mL |
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Buffer | pH: 8.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 64.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |