+Open data
-Basic information
Entry | Database: PDB / ID: 8xvd | ||||||
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Title | CryoEM structure of ADP-DNA-MuB conformation2 | ||||||
Components | ATP-dependent target DNA activator B | ||||||
Keywords | VIRAL PROTEIN / ADP-MuB complex / D10 symmetry / Ring | ||||||
Function / homology | Function and homology information DNA transposition / viral DNA genome replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / DNA integration / DNA replication / host cell cytoplasm / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia phage Mu (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.43 Å | ||||||
Authors | Zhao, X. / Zhang, K. / Li, S. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Elucidating the Architectural dynamics of MuB filaments in bacteriophage Mu DNA transposition. Authors: Xiaolong Zhao / Yongxiang Gao / Qingguo Gong / Kaiming Zhang / Shanshan Li / Abstract: MuB is a non-specific DNA-binding protein and AAA+ ATPase that significantly influences the DNA transposition process of bacteriophage Mu, especially in target DNA selection for transposition. While ...MuB is a non-specific DNA-binding protein and AAA+ ATPase that significantly influences the DNA transposition process of bacteriophage Mu, especially in target DNA selection for transposition. While studies have established the ATP-dependent formation of MuB filament as pivotal to this process, the high-resolution structure of a full-length MuB protomer and the underlying molecular mechanisms governing its oligomerization remain elusive. Here, we use cryo-EM to obtain a 3.4-Å resolution structure of the ATP(+)-DNA(+)-MuB helical filament, which encapsulates the DNA substrate within its axial channel. The structure categorizes MuB within the initiator clade of the AAA+ protein family and precisely locates the ATP and DNA binding sites. Further investigation into the oligomeric states of MuB show the existence of various forms of the filament. These findings lead to a mechanistic model where MuB forms opposite helical filaments along the DNA, exposing potential target sites on the bare DNA and then recruiting MuA, which stimulates MuB's ATPase activity and disrupts the previously formed helical structure. When this happens, MuB generates larger ring structures and dissociates from the DNA. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xvd.cif.gz | 803 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xvd.ent.gz | 678.3 KB | Display | PDB format |
PDBx/mmJSON format | 8xvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xvd_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 8xvd_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 8xvd_validation.xml.gz | 136.9 KB | Display | |
Data in CIF | 8xvd_validation.cif.gz | 160.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/8xvd ftp://data.pdbj.org/pub/pdb/validation_reports/xv/8xvd | HTTPS FTP |
-Related structure data
Related structure data | 38697MC 8xvbC 8xvcC 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: 35153.133 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage Mu (virus) / Gene: B, Mup04 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P03763, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: Chemical | ChemComp-ADP / 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: ADP-DNA-MuB conformation2 with D10 in Bacteriophage Mu DNA Transposition Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia phage Mu (virus) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.8 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 60.9 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 9510 |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67932 / Symmetry type: POINT | ||||||||||||||||||||||||
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