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Yorodumi- EMDB-15126: RuvAB branch migration motor complexed to the Holliday junction -... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15126 | |||||||||
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Title | RuvAB branch migration motor complexed to the Holliday junction - full tripartite particle [dataset t2] | |||||||||
Map data | RuvAB branch migration motor complexed to the Holliday junction - full tripartite particle [dataset t2] | |||||||||
Sample |
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Keywords | DNA recombination / DNA repair / branch migration / Holliday junction / helicase / DNA BINDING PROTEIN | |||||||||
Biological species | Streptococcus thermophilus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||
Authors | Wald J / Marlovits TC | |||||||||
Funding support | 1 items
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Citation | Journal: Nature / Year: 2022 Title: Mechanism of AAA+ ATPase-mediated RuvAB-Holliday junction branch migration. Authors: Jiri Wald / Dirk Fahrenkamp / Nikolaus Goessweiner-Mohr / Wolfgang Lugmayr / Luciano Ciccarelli / Oliver Vesper / Thomas C Marlovits / Abstract: The Holliday junction is a key intermediate formed during DNA recombination across all kingdoms of life. In bacteria, the Holliday junction is processed by two homo-hexameric AAA+ ATPase RuvB motors, ...The Holliday junction is a key intermediate formed during DNA recombination across all kingdoms of life. In bacteria, the Holliday junction is processed by two homo-hexameric AAA+ ATPase RuvB motors, which assemble together with the RuvA-Holliday junction complex to energize the strand-exchange reaction. Despite its importance for chromosome maintenance, the structure and mechanism by which this complex facilitates branch migration are unknown. Here, using time-resolved cryo-electron microscopy, we obtained structures of the ATP-hydrolysing RuvAB complex in seven distinct conformational states, captured during assembly and processing of a Holliday junction. Five structures together resolve the complete nucleotide cycle and reveal the spatiotemporal relationship between ATP hydrolysis, nucleotide exchange and context-specific conformational changes in RuvB. Coordinated motions in a converter formed by DNA-disengaged RuvB subunits stimulate hydrolysis and nucleotide exchange. Immobilization of the converter enables RuvB to convert the ATP-contained energy into a lever motion, which generates the pulling force driving the branch migration. We show that RuvB motors rotate together with the DNA substrate, which, together with a progressing nucleotide cycle, forms the mechanistic basis for DNA recombination by continuous branch migration. Together, our data decipher the molecular principles of homologous recombination by the RuvAB complex, elucidate discrete and sequential transition-state intermediates for chemo-mechanical coupling of hexameric AAA+ motors and provide a blueprint for the design of state-specific compounds targeting AAA+ motors. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15126.map.gz | 14.2 MB | EMDB map data format | |
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Header (meta data) | emd-15126-v30.xml emd-15126.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15126_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_15126.png | 42 KB | ||
Filedesc metadata | emd-15126.cif.gz | 4.3 KB | ||
Others | emd_15126_half_map_1.map.gz emd_15126_half_map_2.map.gz | 142 MB 142 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15126 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15126 | HTTPS FTP |
-Related structure data
Related structure data | 7pblC 7pbmC 7pbnC 7pboC 7pbpC 7pbqC 7pbrC 7pbsC 7pbtC 7pbuC C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15126.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | RuvAB branch migration motor complexed to the Holliday junction - full tripartite particle [dataset t2] | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: RuvAB branch migration motor complexed to the Holliday...
File | emd_15126_half_map_1.map | ||||||||||||
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Annotation | RuvAB branch migration motor complexed to the Holliday junction - full tripartite particle - half map [dataset t2] | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RuvAB branch migration motor complexed to the Holliday...
File | emd_15126_half_map_2.map | ||||||||||||
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Annotation | RuvAB branch migration motor complexed to the Holliday junction - full tripartite particle - half map [dataset t2] | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RuvAB branch migration motor complexed to the Holliday junction [t2]
Entire | Name: RuvAB branch migration motor complexed to the Holliday junction [t2] |
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Components |
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-Supramolecule #1: RuvAB branch migration motor complexed to the Holliday junction [t2]
Supramolecule | Name: RuvAB branch migration motor complexed to the Holliday junction [t2] type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: RuvAB branch migration complex |
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Source (natural) | Organism: Streptococcus thermophilus (bacteria) |
Molecular weight | Theoretical: 650 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.15 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | in-vitro reconstituted freshly before vitrification |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number real images: 30083 / Average exposure time: 5.0 sec. / Average electron dose: 30.7 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |