6XSS | pdb_00006xss

CryoEM structure of designed helical fusion protein C4_nat_HFuse-7900

• PDB DOI: https://doi.org/10.2210/pdb6XSS/pdb
• EM Map EMD-22305: EMDB EMDataResource

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-07-16 Released: 2020-12-23 
• Deposition Author(s): Redler, R.L., Edman, N.I., Baker, D., Ekiert, D., Bhabha, G.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Design of multi-scale protein complexes by hierarchical building block fusion.

Hsia, Y., Mout, R., Sheffler, W., Edman, N.I., Vulovic, I., Park, Y.J., Redler, R.L., Bick, M.J., Bera, A.K., Courbet, A., Kang, A., Brunette, T.J., Nattermann, U., Tsai, E., Saleem, A., Chow, C.M., Ekiert, D., Bhabha, G., Veesler, D., Baker, D.

(2021) Nat Commun 12: 2294-2294

• PubMed: 33863889 
• DOI: https://doi.org/10.1038/s41467-021-22276-z
• Primary Citation Related Structures: 
  6XH5, 6XI6, 6XNS, 6XSS, 6XT4


• PubMed Abstract: 
  

  A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA, USA.
Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA.
Medical Scientist Training Program, University of Washington, Seattle, WA, USA.
Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA.
Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.
Department of Microbiology, New York University School of Medicine, New York, NY, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 114.83 kDa 
• Atom Count: 8,048 
• Modeled Residue Count: 1,040 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C4_nat_HFuse-7900	A, B, C, D	260	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.16

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Redler, R.L., Edman, N.I., Baker, D., Ekiert, D., Bhabha, G.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1629214

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2021-06-02
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references