+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38695 | |||||||||
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Title | Cryo-EM structure of ATP-DNA-MuB filaments | |||||||||
Map data | CryoEM structure of ATP-DNA-MuB Filaments in Bacteriophage Mu DNA Transposition | |||||||||
Sample |
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Keywords | VIRAL PROTEIN-DNA COMPLEX | |||||||||
Function / homology | Function and homology information DNA transposition / viral DNA genome replication / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / DNA integration / host cell cytoplasm / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Escherichia phage Mu (virus) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Zhao X / Zhang K / Li S | |||||||||
Funding support | 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38695.map.gz | 70.4 MB | EMDB map data format | |
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Header (meta data) | emd-38695-v30.xml emd-38695.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
Images | emd_38695.png | 61.8 KB | ||
Filedesc metadata | emd-38695.cif.gz | 5.6 KB | ||
Others | emd_38695_additional_1.map.gz emd_38695_half_map_1.map.gz emd_38695_half_map_2.map.gz | 136.5 MB 134.3 MB 134.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38695 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38695 | HTTPS FTP |
-Validation report
Summary document | emd_38695_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_38695_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_38695_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | emd_38695_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38695 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38695 | HTTPS FTP |
-Related structure data
Related structure data | 8xvbMC 8xvcC 8xvdC 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_38695.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM structure of ATP-DNA-MuB Filaments in Bacteriophage Mu DNA Transposition | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: CryoEM structure of ATP-DNA-MuB Filaments in Bacteriophage Mu...
File | emd_38695_additional_1.map | ||||||||||||
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Annotation | CryoEM structure of ATP-DNA-MuB Filaments in Bacteriophage Mu DNA Transposition | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoEM structure of ATP-DNA-MuB Filaments in Bacteriophage Mu...
File | emd_38695_half_map_1.map | ||||||||||||
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Annotation | CryoEM structure of ATP-DNA-MuB Filaments in Bacteriophage Mu DNA Transposition | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoEM structure of ATP-DNA-MuB Filaments in Bacteriophage Mu...
File | emd_38695_half_map_2.map | ||||||||||||
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Annotation | CryoEM structure of ATP-DNA-MuB Filaments in Bacteriophage Mu DNA Transposition | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ATP-DNA-MuB Filaments in Bacteriophage Mu DNA Transposition
Entire | Name: ATP-DNA-MuB Filaments in Bacteriophage Mu DNA Transposition |
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Components |
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-Supramolecule #1: ATP-DNA-MuB Filaments in Bacteriophage Mu DNA Transposition
Supramolecule | Name: ATP-DNA-MuB Filaments in Bacteriophage Mu DNA Transposition type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Escherichia phage Mu (virus) |
-Macromolecule #1: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP...
Macromolecule | Name: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia phage Mu (virus) |
Molecular weight | Theoretical: 7.472007 KDa |
Sequence | String: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA) |
-Macromolecule #3: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP...
Macromolecule | Name: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia phage Mu (virus) |
Molecular weight | Theoretical: 7.25567 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT) |
-Macromolecule #2: ATP-dependent target DNA activator B
Macromolecule | Name: ATP-dependent target DNA activator B / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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Source (natural) | Organism: Escherichia phage Mu (virus) |
Molecular weight | Theoretical: 35.153133 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MNISDIRAGL RTLVENEETT FKQIALESGL STGTISSFIN DKYNGDNERV SQMLQRWLEK YHAVAELPEP PRFVETQTVK QIWTSMRFA SLTESIAVVC GNPGVGKTEA AREYRRTNNN VWMITITPSC ASVLECLTEL AFELGMNDAP RRKGPLSRAL R RRLEGTQG ...String: MNISDIRAGL RTLVENEETT FKQIALESGL STGTISSFIN DKYNGDNERV SQMLQRWLEK YHAVAELPEP PRFVETQTVK QIWTSMRFA SLTESIAVVC GNPGVGKTEA AREYRRTNNN VWMITITPSC ASVLECLTEL AFELGMNDAP RRKGPLSRAL R RRLEGTQG LVIIDEADHL GAEVLEELRL LQESTRIGLV LMGNHRVYSN MTGGNRTVEF ARLFSRIAKR TAINKTKKAD VK AIADAWQ INGEKELELL QQIAQKPGAL RILNHSLRLA AMTAHGKGER VNEDYLRQAF RELDLDVDIS TLLRN UniProtKB: ATP-dependent target DNA activator B |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 6298 / Average electron dose: 60.9 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: 3.0 µm / Nominal defocus min: 2.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 6.91 Å Applied symmetry - Helical parameters - Δ&Phi: 56.16 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 377689 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |