6E9V | pdb_00006e9v

DHF79 filament

• PDB DOI: https://doi.org/10.2210/pdb6E9V/pdb
• EM Map EMD-9018: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-01 Released: 2018-11-21 
• Deposition Author(s): Lynch, E.M., Shen, H., Fallas, J.A., Kollman, J.M., Baker, D.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.90 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

De novo design of self-assembling helical protein filaments.

Shen, H., Fallas, J.A., Lynch, E., Sheffler, W., Parry, B., Jannetty, N., Decarreau, J., Wagenbach, M., Vicente, J.J., Chen, J., Wang, L., Dowling, Q., Oberdorfer, G., Stewart, L., Wordeman, L., De Yoreo, J., Jacobs-Wagner, C., Kollman, J., Baker, D.

(2018) Science 362: 705-709

• PubMed: 30409885 
• DOI: https://doi.org/10.1126/science.aau3775
• Primary Citation Related Structures: 
  6E9R, 6E9T, 6E9V, 6E9X, 6E9Y, 6E9Z


• PubMed Abstract: 
  

  We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo-electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.

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Organizational Affiliation: 
• Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Molecular Engineering Ph.D. Program, University of Washington, Seattle, WA 98195, USA.
Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. [e-mail] [e-mail].
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.
Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA.
Howard Hughes Medical Institute, Yale University, West Haven, CT 06516, USA.
Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA.
Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA.
Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China.
Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 26-mer - A26 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 600.91 kDa 
• Atom Count: 42,016 
• Modeled Residue Count: 5,486 
• Deposited Residue Count: 5,486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DHF79 filament	A [auth Q], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O [auth N], P [auth O], Q [auth P], R, S, T, U, V, W, X, Y, Z	211	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.90 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-21 
Deposition Author(s): Lynch, E.M., Shen, H., Fallas, J.A., Kollman, J.M., Baker, D.

Revision History  

• Version 1.0: 2018-11-21
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references