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- EMDB-38697: CryoEM structure of ADP-DNA-MuB conformation2 -

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Basic information

Entry
Database: EMDB / ID: EMD-38697
TitleCryoEM structure of ADP-DNA-MuB conformation2
Map dataCryoEM structure of ADP-DNA-MuB conformation2 with D10
Sample
  • Complex: ADP-DNA-MuB conformation2 with D10 in Bacteriophage Mu DNA Transposition
    • Protein or peptide: ATP-dependent target DNA activator B
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsADP-MuB complex / D10 symmetry / 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 / host cell cytoplasm / DNA replication / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
B transposition protein, C-terminal / B transposition protein, C-terminal domain superfamily / Mu B transposition protein, C terminal / : / : / AAA domain / Lambda repressor-like, DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent target DNA activator B
Similarity search - Component
Biological speciesEscherichia phage Mu (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.43 Å
AuthorsZhao X / Zhang K / Li S
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: 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
DepositionJan 14, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38697.png

Downloads & links

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Map

FileDownload / File: emd_38697.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of ADP-DNA-MuB conformation2 with D10
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.16554049 - 0.39430767
Average (Standard dev.)-0.000037257847 (±0.014830225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CryoEM structure of ADP-DNA-MuB conformation2 with D10

Fileemd_38697_additional_1.map
AnnotationCryoEM structure of ADP-DNA-MuB conformation2 with D10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CryoEM structure of ADP-DNA-MuB conformation2 monomer

Fileemd_38697_additional_2.map
AnnotationCryoEM structure of ADP-DNA-MuB conformation2 monomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM structure of ADP-DNA-MuB conformation2 with D10

Fileemd_38697_half_map_1.map
AnnotationCryoEM structure of ADP-DNA-MuB conformation2 with D10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM structure of ADP-DNA-MuB conformation2 with D10

Fileemd_38697_half_map_2.map
AnnotationCryoEM structure of ADP-DNA-MuB conformation2 with D10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ADP-DNA-MuB conformation2 with D10 in Bacteriophage Mu DNA Transp...

EntireName: ADP-DNA-MuB conformation2 with D10 in Bacteriophage Mu DNA Transposition
Components
  • Complex: ADP-DNA-MuB conformation2 with D10 in Bacteriophage Mu DNA Transposition
    • Protein or peptide: ATP-dependent target DNA activator B
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: ADP-DNA-MuB conformation2 with D10 in Bacteriophage Mu DNA Transp...

SupramoleculeName: ADP-DNA-MuB conformation2 with D10 in Bacteriophage Mu DNA Transposition
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia phage Mu (virus)

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Macromolecule #1: ATP-dependent target DNA activator B

MacromoleculeName: ATP-dependent target DNA activator B / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 35.153133 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 20 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 9510 / Average electron dose: 60.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67932
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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