9KZO | pdb_00009kzo

Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 3

• PDB DOI: https://doi.org/10.2210/pdb9KZO/pdb
• EM Map EMD-62666: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Latrodectus hesperus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-11 Released: 2025-12-17 
• Deposition Author(s): Zhang, Y.L., Dai, B.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.08 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Cryo-EM structure of amyloid peptide-silk block protein fibril, Type 3

Zhang, Y.L., Dai, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 15-mer - A6B3C3D3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 15-mer - A3B3C1D1E1F1G1H1I1J1K1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - D2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - D2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 726.08 kDa 
• Atom Count: 1,638 
• Modeled Residue Count: 273 
• Deposited Residue Count: 8,475 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
silk-G6V	A [auth B], B [auth E], C [auth N], D [auth H], E [auth K], F [auth A], G [auth D], H [auth M], I [auth G], J, K [auth C], L [auth F], M [auth O], N [auth I], O [auth L]	565	Latrodectus hesperus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.08 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.15.2_3472

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Zhang, Y.L., Dai, B.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release