+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33013 | |||||||||
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Title | CryoEM structure of RuvA-Holliday junction complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RuvA / Holliday junction / Homologous recombination / DNA damage repair / DNA BINDING PROTEIN-DNA COMPLEX | |||||||||
Function / homology | Function and homology information Holliday junction helicase complex / Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / DNA recombination / DNA repair / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.01 Å | |||||||||
Authors | Lin Z / Qu Q / Zhang X / Zhou Z | |||||||||
Funding support | China, 2 items
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Citation | Journal: Front Plant Sci / Year: 2023 Title: Cryo-EM structure of the RuvAB-Holliday junction intermediate complex from . Authors: Xu Zhang / Zixuan Zhou / Lin Dai / Yulin Chao / Zheng Liu / Mingdong Huang / Qianhui Qu / Zhonghui Lin / Abstract: Holliday junction (HJ) is a four-way structured DNA intermediate in homologous recombination. In bacteria, the HJ-specific binding protein RuvA and the motor protein RuvB together form the RuvAB ...Holliday junction (HJ) is a four-way structured DNA intermediate in homologous recombination. In bacteria, the HJ-specific binding protein RuvA and the motor protein RuvB together form the RuvAB complex to catalyze HJ branch migration. (, Pa) is a ubiquitous opportunistic bacterial pathogen that can cause serious infection in a variety of host species, including vertebrate animals, insects and plants. Here, we describe the cryo-Electron Microscopy (cryo-EM) structure of the RuvAB-HJ intermediate complex from . The structure shows that two RuvA tetramers sandwich HJ at the junction center and disrupt base pairs at the branch points of RuvB-free HJ arms. Eight RuvB subunits are recruited by the RuvA octameric core and form two open-rings to encircle two opposite HJ arms. Each RuvB subunit individually binds a RuvA domain III. The four RuvB subunits within the ring display distinct subdomain conformations, and two of them engage the central DNA duplex at both strands with their C-terminal β-hairpins. Together with the biochemical analyses, our structure implicates a potential mechanism of RuvB motor assembly onto HJ DNA. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33013.map.gz | 217.1 MB | EMDB map data format | |
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Header (meta data) | emd-33013-v30.xml emd-33013.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
Images | emd_33013.png | 12.8 KB | ||
Others | emd_33013_half_map_1.map.gz emd_33013_half_map_2.map.gz | 391.1 MB 391.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33013 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33013 | HTTPS FTP |
-Validation report
Summary document | emd_33013_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_33013_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_33013_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_33013_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33013 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33013 | HTTPS FTP |
-Related structure data
Related structure data | 7x5aMC 7x5bC 7x7pC 7x7qC 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_33013.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33013_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33013_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
-Entire : RuvA-Holliday junction complex
Entire | Name: RuvA-Holliday junction complex |
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Components |
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-Supramolecule #1: RuvA-Holliday junction complex
Supramolecule | Name: RuvA-Holliday junction complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Holliday junction
Supramolecule | Name: Holliday junction / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4 |
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-Supramolecule #3: RuvA
Supramolecule | Name: RuvA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5 |
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Source (natural) | Organism: Pseudomonas aeruginosa PAO1 (bacteria) |
-Macromolecule #1: DNA (26-MER)
Macromolecule | Name: DNA (26-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 7.999266 KDa |
Sequence | String: (DA)(DA)(DA)(DA)(DT)(DA)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DT)(DA)(DA)(DT)(DA)(DT)(DT) (DA)(DT)(DA)(DA)(DT)(DA) |
-Macromolecule #2: DNA (26-MER)
Macromolecule | Name: DNA (26-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 7.972225 KDa |
Sequence | String: (DT)(DA)(DT)(DT)(DA)(DT)(DA)(DA)(DT)(DA) (DT)(DT)(DA)(DA)(DA)(DT)(DA)(DT)(DT)(DA) (DT)(DA)(DT)(DT)(DT)(DA) |
-Macromolecule #3: DNA (26-MER)
Macromolecule | Name: DNA (26-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 7.981238 KDa |
Sequence | String: (DA)(DA)(DA)(DA)(DT)(DT)(DA)(DA)(DT)(DA) (DT)(DT)(DA)(DA)(DA)(DT)(DA)(DT)(DT)(DA) (DT)(DA)(DT)(DT)(DT)(DT) |
-Macromolecule #4: DNA (26-MER)
Macromolecule | Name: DNA (26-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 7.972224 KDa |
Sequence | String: (DT)(DA)(DA)(DA)(DT)(DA)(DT)(DA)(DA)(DT) (DA)(DT)(DT)(DT)(DA)(DA)(DT)(DA)(DT)(DT) (DA)(DA)(DT)(DT)(DT)(DT) |
-Macromolecule #5: Holliday junction ATP-dependent DNA helicase RuvA
Macromolecule | Name: Holliday junction ATP-dependent DNA helicase RuvA / type: protein_or_peptide / ID: 5 / Number of copies: 8 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 |
Molecular weight | Theoretical: 15.432009 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MIGRLRGTLA EKQPPHLILD VNGVGYEVEV PMTTLYRLPS VGEPVTLHTH LVVREDAHLL YGFAEKRERE LFRELIRLNG VGPKLALAL MSGLEVDELV RCVQAQDTST LVKIPGVGKK TAERLLVELK DRFKAWEN UniProtKB: Holliday junction branch migration complex subunit RuvA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 260.0 kPa |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 60241 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 143397 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1) |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7x5a: |