Yorodumi
- EMDB-38696: CryoEM structure of ADP-DNA-MuB conformation1 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38696 | |||||||||
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Title | CryoEM structure of ADP-DNA-MuB conformation1 | |||||||||
Map data | CryoEM structure of ADP-DNA-MuB conformation1 with D9 | |||||||||
Sample |
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Keywords | MuB / MuB-ADP / Ring / VIRAL PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 4.32 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_38696.map.gz | 202.9 MB | EMDB map data format | |
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Header (meta data) | emd-38696-v30.xml emd-38696.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
Images | emd_38696.png | 54.2 KB | ||
Filedesc metadata | emd-38696.cif.gz | 5.3 KB | ||
Others | emd_38696_additional_1.map.gz emd_38696_additional_2.map.gz emd_38696_half_map_1.map.gz emd_38696_half_map_2.map.gz | 203 MB 101.9 MB 199.7 MB 199.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38696 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38696 | HTTPS FTP |
-Related structure data
Related structure data | 8xvcMC 8xvbC 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_38696.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM structure of ADP-DNA-MuB conformation1 with D9 | ||||||||||||||||||||||||||||||||||||
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 ADP-DNA-MuB conformation1 monomer
File | emd_38696_additional_1.map | ||||||||||||
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Annotation | CryoEM structure of ADP-DNA-MuB conformation1 monomer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: CryoEM structure of ADP-DNA-MuB conformation1 with D9
File | emd_38696_additional_2.map | ||||||||||||
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Annotation | CryoEM structure of ADP-DNA-MuB conformation1 with D9 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoEM structure of ADP-DNA-MuB conformation1 with D9
File | emd_38696_half_map_1.map | ||||||||||||
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Annotation | CryoEM structure of ADP-DNA-MuB conformation1 with D9 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CryoEM structure of ADP-DNA-MuB conformation1 with D9
File | emd_38696_half_map_2.map | ||||||||||||
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Annotation | CryoEM structure of ADP-DNA-MuB conformation1 with D9 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ADP-DNA-MuB conformation1
Entire | Name: ADP-DNA-MuB conformation1 |
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Components |
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-Supramolecule #1: ADP-DNA-MuB conformation1
Supramolecule | Name: ADP-DNA-MuB conformation1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia phage Mu (virus) |
-Macromolecule #1: ATP-dependent target DNA activator B
Macromolecule | Name: ATP-dependent target DNA activator B / type: protein_or_peptide / ID: 1 / Number of copies: 18 / 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(DE3) (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 #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 18 / 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
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: 9510 / 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
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: D9 (2x9 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91427 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |