[English] 日本語
![](img/lk-miru.gif)
- EMDB-13303: RuvAB branch migration motor complexed to the Holliday junction -... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | RuvAB branch migration motor complexed to the Holliday junction - RuvA-HJ core [t2 dataset] | |||||||||
![]() | RuvA-HJ core [t2 dataset] | |||||||||
![]() |
| |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Wald J / Marlovits TC | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 10.5 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 14.1 KB 14.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.8 KB | Display | ![]() |
Images | ![]() | 88.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 352 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 351.6 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pbuMC ![]() 7pblC ![]() 7pbmC ![]() 7pbnC ![]() 7pboC ![]() 7pbpC ![]() 7pbqC ![]() 7pbrC ![]() 7pbsC ![]() 7pbtC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | RuvA-HJ core [t2 dataset] | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-
Sample components
-Entire : RuvAB branch migration motor complexed to the Holliday junction -...
Entire | Name: RuvAB branch migration motor complexed to the Holliday junction - RuvA-HJ core [t2 dataset] |
---|---|
Components |
|
-Supramolecule #1: RuvAB branch migration motor complexed to the Holliday junction -...
Supramolecule | Name: RuvAB branch migration motor complexed to the Holliday junction - RuvA-HJ core [t2 dataset] type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: RuvA helicase |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: Holliday junction ATP-dependent DNA helicase RuvA
Macromolecule | Name: Holliday junction ATP-dependent DNA helicase RuvA / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: DNA helicase |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.860438 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: VIGRLRGIIL EKQPPIVLLE TGGVGYEVHM PMTCFYELPE AGQEAIVFTH FVVREDAQLL YGFNNKQERT LFKELIKTNG VGPKLALAI LSGMSAQQFV NAVEREELGA LVKLPGIGKK TAERLIVEMK DRFK |
-Macromolecule #2: Holliday junction
Macromolecule | Name: Holliday junction / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 5.224434 KDa |
Sequence | String: (DT)(DA)(DT)(DT)(DC)(DT)(DT)(DT)(DA)(DA) (DA)(DG)(DA)(DA)(DT)(DA)(DG) |
-Macromolecule #3: Holliday junction
Macromolecule | Name: Holliday junction / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 5.18441 KDa |
Sequence | String: (DC)(DT)(DA)(DT)(DT)(DC)(DT)(DT)(DT)(DA) (DA)(DA)(DG)(DA)(DA)(DT)(DA) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 |
---|---|
Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.15000000000000002 nm |
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 |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm |
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
-Atomic model buiding 1
Refinement | Protocol: OTHER |
---|---|
Output model | ![]() PDB-7pbu: |