+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11367 | |||||||||
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Title | 16 helix bundle | |||||||||
Map data | 16 helix bundle | |||||||||
Sample |
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Biological species | Escherichia virus M13 / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.0 Å | |||||||||
Authors | Kube M / Kohler F / Feigl E | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution. Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W ...Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W Scheres / Hendrik Dietz / Abstract: The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is ...The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11367.map.gz | 165.9 MB | EMDB map data format | |
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Header (meta data) | emd-11367-v30.xml emd-11367.xml | 51.4 KB 51.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11367_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_11367.png | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11367 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11367 | HTTPS FTP |
-Validation report
Summary document | emd_11367_validation.pdf.gz | 301.8 KB | Display | EMDB validaton report |
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Full document | emd_11367_full_validation.pdf.gz | 300.9 KB | Display | |
Data in XML | emd_11367_validation.xml.gz | 12.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11367 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11367 | HTTPS FTP |
-Related structure data
Related structure data | 7arqMC 7areC 7artC 7arvC 7aryC 7as5C 6zql M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11367.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 16 helix bundle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : 16 helix bundle
+Supramolecule #1: 16 helix bundle
+Supramolecule #2: DNA
+Supramolecule #3: DNA Staple
+Macromolecule #1: DNA Staple
+Macromolecule #2: DNA Staple
+Macromolecule #3: DNA Staple
+Macromolecule #4: DNA Staple
+Macromolecule #5: DNA Staple
+Macromolecule #6: DNA Staple
+Macromolecule #7: DNA Staple
+Macromolecule #8: DNA Staple
+Macromolecule #9: DNA Staple
+Macromolecule #10: DNA Staple
+Macromolecule #11: DNA Staple
+Macromolecule #12: DNA Staple
+Macromolecule #13: DNA Staple
+Macromolecule #14: DNA Staple
+Macromolecule #15: DNA Staple
+Macromolecule #16: DNA Staple
+Macromolecule #17: DNA Staple
+Macromolecule #18: DNA Staple
+Macromolecule #19: DNA Staple
+Macromolecule #20: DNA Staple
+Macromolecule #21: DNA Staple
+Macromolecule #22: DNA Staple
+Macromolecule #23: DNA Staple
+Macromolecule #24: DNA Staple
+Macromolecule #25: DNA Staple
+Macromolecule #26: DNA Staple
+Macromolecule #27: DNA Staple
+Macromolecule #28: DNA Staple
+Macromolecule #29: DNA Staple
+Macromolecule #30: DNA Staple
+Macromolecule #31: DNA Staple
+Macromolecule #32: DNA Staple
+Macromolecule #33: DNA Staple
+Macromolecule #34: DNA Staple
+Macromolecule #35: DNA Staple
+Macromolecule #36: DNA Staple
+Macromolecule #37: DNA Staple
-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: C-flat / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
Details | Monodisperse, 20nM |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Details | Initial model generated by ENRG-MD. Then MDFF in combination with the ENRG-MD elastic network was used for flexible fitting. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | PDB-7arq: |