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Open data
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Basic information
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Title | virus enhancing amyloid fibril formed by CKFKFQF | |||||||||
![]() | postprocessed map | |||||||||
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![]() | virus enhancing amyloid fibril / protein fibril / prion | |||||||||
Biological species | synthetic construct (others) / HIV whole-genome vector AA1305#18 (others) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
![]() | Heerde T / Schmidt M / Faendrich M | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure and polymorphic maturation of a viral transduction enhancing amyloid fibril. Authors: Thomas Heerde / Desiree Schütz / Yu-Jie Lin / Jan Münch / Matthias Schmidt / Marcus Fändrich / ![]() Abstract: Amyloid fibrils have emerged as innovative tools to enhance the transduction efficiency of retroviral vectors in gene therapy strategies. In this study, we used cryo-electron microscopy to analyze ...Amyloid fibrils have emerged as innovative tools to enhance the transduction efficiency of retroviral vectors in gene therapy strategies. In this study, we used cryo-electron microscopy to analyze the structure of a biotechnologically engineered peptide fibril that enhances retroviral infectivity. Our findings show that the peptide undergoes a time-dependent morphological maturation into polymorphic amyloid fibril structures. The fibrils consist of mated cross-β sheets that interact by the hydrophobic residues of the amphipathic fibril-forming peptide. The now available structural data help to explain the mechanism of retroviral infectivity enhancement, provide insights into the molecular plasticity of amyloid structures and illuminate the thermodynamic basis of their morphological maturation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.7 KB 16.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 53.9 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Others | ![]() ![]() ![]() | 95.2 MB 79.2 MB 79.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 693.8 KB | Display | ![]() |
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Full document | ![]() | 693.3 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | postprocessed map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.81 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: Unmasked map
File | emd_16930_additional_1.map | ||||||||||||
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Annotation | Unmasked map | ||||||||||||
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Density Histograms |
-Half map: second half-map
File | emd_16930_half_map_1.map | ||||||||||||
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Annotation | second half-map | ||||||||||||
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Density Histograms |
-Half map: first half-map
File | emd_16930_half_map_2.map | ||||||||||||
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Annotation | first half-map | ||||||||||||
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Sample components
-Entire : virus enhancing amyloid
Entire | Name: virus enhancing amyloid |
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Components |
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-Supramolecule #1: virus enhancing amyloid
Supramolecule | Name: virus enhancing amyloid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: PNF-18
Macromolecule | Name: PNF-18 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: HIV whole-genome vector AA1305#18 (others) |
Molecular weight | Theoretical: 949.168 Da |
Sequence | String: CKFKFQF |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7 / Component - Concentration: 50.0 mM / Component - Formula: C8H18N2O4S Component - Name: 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid Details: 50 mM 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 96 % / Instrument: FEI VITROBOT MARK III |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 8.0 sec. / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE / Target criteria: correlation coefficient |
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Output model | ![]() PDB-8okr: |