+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16930 | |||||||||
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Title | virus enhancing amyloid fibril formed by CKFKFQF | |||||||||
Map data | postprocessed map | |||||||||
Sample |
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Keywords | 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 | |||||||||
Authors | Heerde T / Schmidt M / Faendrich M | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2023 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 | emd_16930.map.gz | 4.4 MB | EMDB map data format | |
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Header (meta data) | emd-16930-v30.xml emd-16930.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16930_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_16930.png | 53.9 KB | ||
Masks | emd_16930_msk_1.map | 103 MB | Mask map | |
Others | emd_16930_additional_1.map.gz emd_16930_half_map_1.map.gz emd_16930_half_map_2.map.gz | 95.2 MB 79.2 MB 79.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16930 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16930 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16930.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_16930_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unmasked map
File | emd_16930_additional_1.map | ||||||||||||
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Annotation | Unmasked map | ||||||||||||
Projections & Slices |
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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 | ||||||||||||
Projections & Slices |
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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 | ||||||||||||
Projections & Slices |
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Density Histograms |
-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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Processing | helical reconstruction |
Aggregation state | helical array |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: BACKBONE TRACE / Target criteria: correlation coefficient |
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Output model | PDB-8okr: |