+Open data
-Basic information
Entry | Database: PDB / ID: 7tqd | |||||||||
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Title | Structure of Enterobacter cloacae Cap2-CdnD02 2:1 complex | |||||||||
Components |
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Keywords | TRANSFERASE / CBASS / ubiquitin E1/E2 / bacterial anti-phage defense / cGAS | |||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Gu, Y. / Ye, Q. / Ledvina, H.E. / Quan, Y. / Lau, R.K. / Zhou, H. / Whiteley, A.T. / Corbett, K.D. | |||||||||
Funding support | United States, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tqd.cif.gz | 281.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tqd.ent.gz | 180.2 KB | Display | PDB format |
PDBx/mmJSON format | 7tqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tqd_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7tqd_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7tqd_validation.xml.gz | 50.9 KB | Display | |
Data in CIF | 7tqd_validation.cif.gz | 74.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/7tqd ftp://data.pdbj.org/pub/pdb/validation_reports/tq/7tqd | HTTPS FTP |
-Related structure data
Related structure data | 26066MC 7to3C 7tsqC 7tsxC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 67024.953 Da / Num. of mol.: 2 / Mutation: C109A, C548A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Production host: Escherichia coli (E. coli) #2: Protein | | Mass: 45506.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: cdnD02, P853_02262 / Production host: Escherichia coli (E. coli) References: UniProt: P0DSP4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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-Non-polymers , 4 types, 5 molecules
#3: Chemical | ChemComp-AMP / | ||||
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#4: Chemical | #5: Chemical | ChemComp-ATP / | #6: Chemical | ChemComp-ADP / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary complex of Cap2 and CdnD02 in a 2:1 stoichiometry. Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.1794 MDa / Experimental value: NO |
Source (natural) | Organism: Enterobacter cloacae (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8.5 |
Specimen | Conc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Average exposure time: 10 sec. / Electron dose: 64.8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147709 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7LJL Pdb chain-ID: A | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 116.19 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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