+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28107 | |||||||||
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Title | Structure of double homo-hexameric AAA+ ATPase RuvB motors | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information 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 | Thermus thermophilus HB8 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.16 Å | |||||||||
Authors | Shen ZF / Rish AD / Fu TM | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Structure of double homo-hexameric AAA+ ATPase RuvB motor binding with DNA substrate Authors: Rish AD / Shen ZF / Fu TM | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28107.map.gz | 36.2 MB | EMDB map data format | |
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Header (meta data) | emd-28107-v30.xml emd-28107.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28107_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_28107.png | 120.6 KB | ||
Masks | emd_28107_msk_1.map | 38.4 MB | Mask map | |
Others | emd_28107_half_map_1.map.gz emd_28107_half_map_2.map.gz | 35.5 MB 35.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28107 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28107 | HTTPS FTP |
-Validation report
Summary document | emd_28107_validation.pdf.gz | 942 KB | Display | EMDB validaton report |
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Full document | emd_28107_full_validation.pdf.gz | 941.5 KB | Display | |
Data in XML | emd_28107_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | emd_28107_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28107 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28107 | HTTPS FTP |
-Related structure data
Related structure data | 8efyMC 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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-Map
File | Download / File: emd_28107.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-Mask #1
File | emd_28107_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_28107_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_28107_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Double homo-hexameric AAA+ ATPase RuvB motors
Entire | Name: Double homo-hexameric AAA+ ATPase RuvB motors |
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Components |
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-Supramolecule #1: Double homo-hexameric AAA+ ATPase RuvB motors
Supramolecule | Name: Double homo-hexameric AAA+ ATPase RuvB motors / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) |
-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: 12 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8 |
Molecular weight | Theoretical: 36.024688 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 |
-Macromolecule #2: ssDNA
Macromolecule | Name: ssDNA / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) |
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: ssDNA
Macromolecule | Name: ssDNA / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) |
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: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 6 / Formula: AGS |
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Molecular weight | Theoretical: 523.247 Da |
Chemical component information | ChemComp-AGS: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN 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: FIELD EMISSION GUN |
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 |