+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40036 | ||||||||||||
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Title | RuvA Holliday junction DNA complex | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Holliday junction / tetramer / RuvA / DNA BINDING PROTEIN / 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 | Thermus thermophilus HB8 (bacteria) / Punavirus P1 / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||||||||
Authors | Rish AD / Fu T | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Protein Sci / Year: 2018 Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin / Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40036.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-40036-v30.xml emd-40036.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40036_fsc.xml | 11.7 KB | Display | FSC data file |
Images | emd_40036.png | 52.1 KB | ||
Filedesc metadata | emd-40036.cif.gz | 5.5 KB | ||
Others | emd_40036_half_map_1.map.gz emd_40036_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40036 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40036 | HTTPS FTP |
-Validation report
Summary document | emd_40036_validation.pdf.gz | 736 KB | Display | EMDB validaton report |
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Full document | emd_40036_full_validation.pdf.gz | 735.7 KB | Display | |
Data in XML | emd_40036_validation.xml.gz | 16 KB | Display | |
Data in CIF | emd_40036_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40036 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40036 | HTTPS FTP |
-Related structure data
Related structure data | 8gh8MC 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_40036.map.gz / Format: CCP4 / Size: 64 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: 0.95 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_40036_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40036_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RuvA DNA binding protein complexed with Holliday Junction DNA
Entire | Name: RuvA DNA binding protein complexed with Holliday Junction DNA |
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Components |
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-Supramolecule #1: RuvA DNA binding protein complexed with Holliday Junction DNA
Supramolecule | Name: RuvA DNA binding protein complexed with Holliday Junction DNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) |
-Supramolecule #2: Tetrameric RuvA binding protein
Supramolecule | Name: Tetrameric RuvA binding protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) |
-Supramolecule #3: Holliday Junction DNA adapted from PDB 2HOI
Supramolecule | Name: Holliday Junction DNA adapted from PDB 2HOI / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Punavirus P1 |
-Macromolecule #1: Holliday junction branch migration complex subunit RuvA
Macromolecule | Name: Holliday junction branch migration complex subunit RuvA type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: Thermus thermophilus HB8 (bacteria) |
Molecular weight | Theoretical: 14.933622 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MIRYLRGLVL KKEAGGFVLL AGGVGFFLQA PTPFLQALEE GKEVGVHTHL LLKEEGLSLY GFPDEENLAL FELLLSVSGV GPKVALALL SALPPRLLAR ALLEGDARLL TSASGVGRRL AERIALELKG KVPPHLLAGE K UniProtKB: Holliday junction branch migration complex subunit RuvA |
-Macromolecule #2: DNA (34-MER)
Macromolecule | Name: DNA (34-MER) / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 10.399752 KDa |
Sequence | String: (DA)(DT)(DA)(DA)(DC)(DT)(DT)(DC)(DG)(DT) (DA)(DT)(DA)(DG)(DC)(DA)(DT)(DA)(DC)(DA) (DT)(DT)(DA)(DT)(DA)(DC)(DG)(DA)(DA) (DC)(DT)(DT)(DA)(DT) |
-Macromolecule #3: DNA (34-MER)
Macromolecule | Name: DNA (34-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 10.51081 KDa |
Sequence | String: (DA)(DT)(DA)(DA)(DG)(DT)(DT)(DC)(DG)(DT) (DA)(DT)(DA)(DA)(DT)(DG)(DT)(DA)(DT)(DG) (DC)(DT)(DA)(DT)(DA)(DC)(DG)(DA)(DA) (DG)(DT)(DT)(DA)(DT) |
-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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k 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 |