8OKR | pdb_00008okr

virus enhancing amyloid fibril formed by CKFKFQF

• PDB DOI: https://doi.org/10.2210/pdb8OKR/pdb
• EM Map EMD-16930: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): HIV whole-genome vector AA1305#18
• Mutation(s): No 


• Deposited: 2023-03-29 Released: 2023-08-02 
• Deposition Author(s): Heerde, T., Schmidt, M., Faendrich, M.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.86 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Literature

Cryo-EM structure and polymorphic maturation of a viral transduction enhancing amyloid fibril.

Heerde, T., Schutz, D., Lin, Y.J., Munch, J., Schmidt, M., Fandrich, M.

(2023) Nat Commun 14: 4293-4293

• PubMed: 37464004 
• DOI: https://doi.org/10.1038/s41467-023-40042-1
• Primary Citation Related Structures: 
  8OKR


• PubMed 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 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.

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Organizational Affiliation: 
• Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany. [e-mail].
Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 22.78 kDa 
• Atom Count: 1,608 
• Modeled Residue Count: 168 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PNF-18	A [auth S], B [auth T], C [auth U], D [auth V], E [auth W], F [auth X], G [auth M], H [auth N], I [auth O], J [auth P], K [auth Q], L [auth R], M [auth G], N [auth H], O [auth I], P [auth J], Q [auth K], R [auth L], S [auth A], T [auth B], U [auth C], V [auth D], W [auth E], X [auth F]	7	HIV whole-genome vector AA1305#18	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.86 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.16-3549
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Heerde, T., Schmidt, M., Faendrich, M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	CRC 1279/2 project A03

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Data collection