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- EMDB-16930: virus enhancing amyloid fibril formed by CKFKFQF -

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Basic information

Entry
Database: EMDB / ID: EMD-16930
Titlevirus enhancing amyloid fibril formed by CKFKFQF
Map datapostprocessed map
Sample
  • Complex: virus enhancing amyloid
    • Protein or peptide: PNF-18
Keywordsvirus enhancing amyloid fibril / protein fibril / prion
Biological speciessynthetic construct (others) / HIV whole-genome vector AA1305#18 (others)
Methodhelical reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsHeerde T / Schmidt M / Faendrich M
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC 1279/2 project A03 Germany
CitationJournal: 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
DepositionMar 29, 2023-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16930.png

Downloads & links

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Map

FileDownload / File: emd_16930.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 300 pix.
= 243. Å		0.81 Å/pix.
x 300 pix.
= 243. Å		0.81 Å/pix.
x 300 pix.
= 243. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0165
Minimum - Maximum-0.03004744 - 0.069932766
Average (Standard dev.)0.000037664417 (±0.0009591884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 243.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16930_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Unmasked map

Fileemd_16930_additional_1.map
AnnotationUnmasked map
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Half map: second half-map

Fileemd_16930_half_map_1.map
Annotationsecond half-map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: first half-map

Fileemd_16930_half_map_2.map
Annotationfirst half-map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : virus enhancing amyloid

EntireName: virus enhancing amyloid
Components
  • Complex: virus enhancing amyloid
    • Protein or peptide: PNF-18

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Supramolecule #1: virus enhancing amyloid

SupramoleculeName: virus enhancing amyloid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: PNF-18

MacromoleculeName: PNF-18 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: HIV whole-genome vector AA1305#18 (others)
Molecular weightTheoretical: 949.168 Da
SequenceString:
CKFKFQF

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 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
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 96 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: -2.61 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 25550
Segment selectionNumber selected: 356134
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE / Target criteria: correlation coefficient
Output model

PDB-8okr:
virus enhancing amyloid fibril formed by CKFKFQF

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