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Yorodumi- PDB-7u6v: Cryo-EM structure of Shiga toxin 2 in complex with the native rib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u6v | ||||||
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Title | Cryo-EM structure of Shiga toxin 2 in complex with the native ribosomal P-stalk | ||||||
Components |
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Keywords | TOXIN / Shiga toxin 2 / Ribosomal P-stalk / Complex | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation Similarity search - Function | ||||||
Biological species | Shigella dysenteriae (bacteria) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Kulczyk, A.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Biol Chem / Year: 2023 Title: Cryo-EM structure of Shiga toxin 2 in complex with the native ribosomal P-stalk reveals residues involved in the binding interaction. Authors: Arkadiusz W Kulczyk / Carlos Oscar S Sorzano / Przemysław Grela / Marek Tchórzewski / Nilgun E Tumer / Xiao-Ping Li / Abstract: Shiga toxin 2a (Stx2a) is the virulence factor of enterohemorrhagic Escherichia coli. The catalytic A1 subunit of Stx2a (Stx2A1) interacts with the ribosomal P-stalk for loading onto the ribosome and ...Shiga toxin 2a (Stx2a) is the virulence factor of enterohemorrhagic Escherichia coli. The catalytic A1 subunit of Stx2a (Stx2A1) interacts with the ribosomal P-stalk for loading onto the ribosome and depurination of the sarcin-ricin loop, which halts protein synthesis. Because of the intrinsic flexibility of the P-stalk, a structure of the Stx2a-P-stalk complex is currently unknown. We demonstrated that the native P-stalk pentamer binds to Stx2a with nanomolar affinity, and we employed cryo-EM to determine a structure of the 72 kDa Stx2a complexed with the P-stalk. The structure identifies Stx2A1 residues involved in binding and reveals that Stx2a is anchored to the P-stalk via only the last six amino acids from the C-terminal domain of a single P-protein. For the first time, the cryo-EM structure shows the loop connecting Stx2A1 and Stx2A2, which is critical for activation of the toxin. Our principal component analysis of the cryo-EM data reveals the intrinsic dynamics of the Stx2a-P-stalk interaction, including conformational changes in the P-stalk binding site occurring upon complex formation. Our computational analysis unveils the propensity for structural rearrangements within the C-terminal domain, with its C-terminal six amino acids transitioning from a random coil to an α-helix upon binding to Stx2a. In conclusion, our cryo-EM structure sheds new light into the dynamics of the Stx2a-P-stalk interaction and indicates that the binding interface between Stx2a and the P-stalk is the potential target for drug discovery. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u6v.cif.gz | 250.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u6v.ent.gz | 198.8 KB | Display | PDB format |
PDBx/mmJSON format | 7u6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u6v_validation.pdf.gz | 931.6 KB | Display | wwPDB validaton report |
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Full document | 7u6v_full_validation.pdf.gz | 941.8 KB | Display | |
Data in XML | 7u6v_validation.xml.gz | 36.3 KB | Display | |
Data in CIF | 7u6v_validation.cif.gz | 52.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/7u6v ftp://data.pdbj.org/pub/pdb/validation_reports/u6/7u6v | HTTPS FTP |
-Related structure data
Related structure data | 26381MC M: map data used to model this data C: citing same article (ref.) |
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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
#1: Protein | Mass: 33214.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella dysenteriae (bacteria) / Gene: stxA2 / Production host: Escherichia coli (E. coli) / References: UniProt: G8GWP6, rRNA N-glycosylase | ||||
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#2: Protein | Mass: 7824.590 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella dysenteriae (bacteria) / Production host: Escherichia coli (E. coli) #3: Protein/peptide | | Mass: 654.712 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 0.1 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 1.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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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: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112924 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||||||||
Refine LS restraints |
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