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

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Basic information

Entry
Database: PDB / ID: 8okr
Titlevirus enhancing amyloid fibril formed by CKFKFQF
ComponentsPNF-18
KeywordsPROTEIN FIBRIL / virus enhancing amyloid fibril / prion
Biological speciesHIV whole-genome vector AA1305#18 (others)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsHeerde, T. / Schmidt, M. / Faendrich, M.
Funding support Germany, 1items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: PNF-18
T: PNF-18
U: PNF-18
V: PNF-18
W: PNF-18
X: PNF-18
M: PNF-18
N: PNF-18
O: PNF-18
P: PNF-18
Q: PNF-18
R: PNF-18
G: PNF-18
H: PNF-18
I: PNF-18
J: PNF-18
K: PNF-18
L: PNF-18
A: PNF-18
B: PNF-18
C: PNF-18
D: PNF-18
E: PNF-18
F: PNF-18


Theoretical massNumber of molelcules
Total (without water)22,78024
Polymers22,78024
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area20610 Å2
ΔGint-113 kcal/mol
Surface area8470 Å2

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Components

#1: Protein/peptide ...
PNF-18


Mass: 949.168 Da / Num. of mol.: 24 / Source method: obtained synthetically / Source: (synth.) HIV whole-genome vector AA1305#18 (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: virus enhancing amyloid / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
Details: 50 mM 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
Buffer componentConc.: 50 mM
Name: 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
Formula: C8H18N2O4S
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 96 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4GctfCTF correction
7Coot0.8.9model fitting
9PHENIX1.16-3549model refinement
12RELION3.0.4classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -2.61 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C2
Particle selectionNum. of particles selected: 356134
3D reconstructionResolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25550 / Symmetry type: HELICAL
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL / Target criteria: correlation coefficient

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