6XH5 | pdb_00006xh5

Hierarchical design of multi-scale protein complexes by combinatorial assembly of oligomeric helical bundle and repeat protein building blocks

• PDB DOI: https://doi.org/10.2210/pdb6XH5/pdb

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


• Deposited: 2020-06-18 Released: 2021-06-02 
• Deposition Author(s): Bera, A.K., Hsia, Y., Kang, A.S., Baker, D.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free: 
  0.265 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: in silico

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 - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 234.72 kDa 
• Atom Count: 15,880 
• Modeled Residue Count: 2,087 
• Deposited Residue Count: 2,154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
helical fusion design	A, B, C, D, E, F	359	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.32 Å
• R-Value Free:  0.265 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.766	α = 90
b = 166.766	β = 90
c = 223.512	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-02 
Deposition Author(s): Bera, A.K., Hsia, Y., Kang, A.S., Baker, D.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2021-06-02
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2024-04-03
  Changes: Refinement description