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- EMDB-28101: Structure of single homo-hexameric Holliday junction ATP-dependen... -
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Open data
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Basic information
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Title | Structure of single homo-hexameric Holliday junction ATP-dependent DNA helicase RuvB motor | |||||||||
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![]() | Holliday Junction / AAA+ ATPase / RuvB / Homo-hexamer / DNA recombination / STRUCTURAL PROTEIN | |||||||||
Function / homology | ![]() Holliday junction resolvase complex / four-way junction helicase activity / four-way junction DNA binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA recombination / DNA repair / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
![]() | Shen ZF / Rish AD / Fu TM | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structure of single homo-hexameric Holliday junction ATP-dependent DNA helicase RuvB motor Authors: Shen ZF / Rish AD / Fu TM | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 36.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.6 KB 15.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.1 KB | Display | ![]() |
Images | ![]() | 66.3 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 35.7 MB 35.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 908.2 KB | Display | ![]() |
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Full document | ![]() | 907.8 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8efvMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_28101_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28101_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Single homo-hexameric AAA+ ATPase RuvB motor
Entire | Name: Single homo-hexameric AAA+ ATPase RuvB motor |
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Components |
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-Supramolecule #1: Single homo-hexameric AAA+ ATPase RuvB motor
Supramolecule | Name: Single homo-hexameric AAA+ ATPase RuvB motor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Holliday junction ATP-dependent DNA helicase RuvB
Macromolecule | Name: Holliday junction ATP-dependent DNA helicase RuvB / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 36.024688 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEDLALRPKT LDEYIGQERL KQKLRVYLEA AKARKEPLEH LLLFGPPGLG KTTLAHVIAH ELGVNLRVTS GPAIEKPGDL AAILANSLE EGDILFIDEI HRLSRQAEEH LYPAMEDFVM DIVIGQGPAA RTIRLELPRF TLIGATTRPG LITAPLLSRF G IVEHLEYY ...String: MEDLALRPKT LDEYIGQERL KQKLRVYLEA AKARKEPLEH LLLFGPPGLG KTTLAHVIAH ELGVNLRVTS GPAIEKPGDL AAILANSLE EGDILFIDEI HRLSRQAEEH LYPAMEDFVM DIVIGQGPAA RTIRLELPRF TLIGATTRPG LITAPLLSRF G IVEHLEYY TPEELAQGVM RDARLLGVRI TEEAALEIGR RSRGTMRVAK RLFRRVRDFA QVAGEEVITR ERALEALAAL GL DELGLEK RDREILEVLI LRFGGGPVGL ATLATALSED PGTLEEVHEP YLIRQGLLKR TPRGRVATEL AYRHLGYPPP VGP LLEP UniProtKB: Holliday junction branch migration complex subunit RuvB |
-Macromolecule #2: 49-mer DNA
Macromolecule | Name: 49-mer DNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.146732 KDa |
Sequence | String: (DA)(DG)(DA)(DA)(DT)(DC)(DT)(DG)(DC)(DC) (DG)(DA)(DG)(DA)(DG)(DA)(DC)(DC)(DG)(DA) (DG)(DC)(DA)(DG)(DA)(DA)(DT)(DT)(DC) (DT)(DA)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DA) (DC) (DC)(DA)(DA)(DG)(DC)(DG)(DC)(DT) (DG) |
-Macromolecule #3: 51-mer DNA
Macromolecule | Name: 51-mer DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.69107 KDa |
Sequence | String: (DC)(DA)(DG)(DC)(DG)(DC)(DT)(DT)(DG)(DG) (DT)(DA)(DA)(DA)(DC)(DA)(DC)(DA)(DT)(DA) (DG)(DA)(DA)(DT)(DT)(DC)(DT)(DG)(DC) (DT)(DC)(DT)(DC)(DG)(DG)(DT)(DC)(DT)(DG) (DA) (DG)(DC)(DC)(DG)(DT)(DC)(DT)(DA) (DA)(DG)(DA) |
-Macromolecule #4: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 3 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ![]() ChemComp-AGS: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 3 / 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |