6E5C | pdb_00006e5c

Solution NMR structure of a de novo designed double-stranded beta-helix

• PDB DOI: https://doi.org/10.2210/pdb6E5C/pdb
• BMRB: 30495

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


• Deposited: 2018-07-19 Released: 2018-11-07 
• Deposition Author(s): Marcos, E., Chidyausiku, T.M., McShan, A., Evangelidis, T., Nerli, S., Sgourakis, N., Tripsianes, K., Baker, D.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

De novo design of a non-local beta-sheet protein with high stability and accuracy.

Marcos, E., Chidyausiku, T.M., McShan, A.C., Evangelidis, T., Nerli, S., Carter, L., Nivon, L.G., Davis, A., Oberdorfer, G., Tripsianes, K., Sgourakis, N.G., Baker, D.

(2018) Nat Struct Mol Biol 25: 1028-1034

• PubMed: 30374087 
• DOI: https://doi.org/10.1038/s41594-018-0141-6
• Primary Citation Related Structures: 
  6E5C


• PubMed Abstract: 
  

  β-sheet proteins carry out critical functions in biology, and hence are attractive scaffolds for computational protein design. Despite this potential, de novo design of all-β-sheet proteins from first principles lags far behind the design of all-α or mixed-αβ domains owing to their non-local nature and the tendency of exposed β-strand edges to aggregate. Through study of loops connecting unpaired β-strands (β-arches), we have identified a series of structural relationships between loop geometry, side chain directionality and β-strand length that arise from hydrogen bonding and packing constraints on regular β-sheet structures. We use these rules to de novo design jellyroll structures with double-stranded β-helices formed by eight antiparallel β-strands. The nuclear magnetic resonance structure of a hyperthermostable design closely matched the computational model, demonstrating accurate control over the β-sheet structure and loop geometry. Our results open the door to the design of a broad range of non-local β-sheet protein structures.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA.
CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA, USA.
Cyrus Biotechnology, Seattle, WA, USA.
Amazon, Seattle, WA, USA.
Institute of Biochemistry, Graz University of Technology, Graz, Austria.
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 8.92 kDa 
• Atom Count: 628 
• Modeled Residue Count: 78 
• Deposited Residue Count: 78 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo beta protein	A	78	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-07 
Deposition Author(s): Marcos, E., Chidyausiku, T.M., McShan, A., Evangelidis, T., Nerli, S., Sgourakis, N., Tripsianes, K., Baker, D.

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Funding Organization	Location	Grant Number
European Commission	Spain	FP7-PEOPLE-2011-IOF 298976

Revision History  

• Version 1.0: 2018-11-07
  Type: Initial release
  
• Version 1.1: 2018-11-14
  Changes: Data collection, Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references