7URJ | pdb_00007urj

Backbone-modified variant of the B domain of Staphylococcal protein A: beta3- and ACPC-residues in helix 2

• PDB DOI: https://doi.org/10.2210/pdb7URJ/pdb
• BMRB: 31012

• Classification: DE NOVO PROTEIN
• Organism(s): Staphylococcus aureus
• Mutation(s): Yes 


• Deposited: 2022-04-22 Released: 2023-05-03 
• Deposition Author(s): Santhouse, J.R., Leung, J.M.G., Chong, L.T., Horne, W.S.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

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

Literature

Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein.

Santhouse, J.R., Leung, J.M.G., Chong, L.T., Horne, W.S.

(2024) Chem Sci 15: 675-682

• PubMed: 38179541 
• DOI: https://doi.org/10.1039/d3sc03976e
• Primary Citation Related Structures: 
  7URJ


• PubMed Abstract: 
  

  Sequence-encoded protein folding is a ubiquitous biological process that has been successfully engineered in a range of oligomeric molecules with artificial backbone chemical connectivity. A remarkable aspect of protein folding is the contrast between the rapid rates at which most sequences in nature fold and the vast number of conformational states possible in an unfolded chain with hundreds of rotatable bonds. Research efforts spanning several decades have sought to elucidate the fundamental chemical principles that dictate the speed and mechanism of natural protein folding. In contrast, little is known about how protein mimetic entities transition between an unfolded and folded state. Here, we report effects of altered backbone connectivity on the folding kinetics and mechanism of the B domain of Staphylococcal protein A (BdpA), an ultrafast-folding sequence. A combination of experimental biophysical analysis and atomistic molecular dynamics simulations performed on the prototype protein and several heterogeneous-backbone variants reveal the interplay among backbone flexibility, folding rates, and structural details of the transition state ensemble. Collectively, these findings suggest a significant degree of plasticity in the mechanisms that can give rise to ultrafast folding in the BdpA sequence and provide atomic level insights into how protein mimetic chains adopt an ordered folded state.

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Organizational Affiliation: 
• Department of Chemistry, University of Pittsburgh Pittsburgh PA 15260 USA [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.61 kDa 
• Atom Count: 466 
• Modeled Residue Count: 59 
• Deposited Residue Count: 59 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Staphylococcal protein A	A	59	Staphylococcus aureus	Mutation(s): 1

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
B3K	A	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS
B3X	A	L-PEPTIDE LINKING	C5 H10 N2 O3		ASN
XCP	A	PEPTIDE-LIKE	C6 H11 N O2		--

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: 2023-05-03 
Deposition Author(s): Santhouse, J.R., Leung, J.M.G., Chong, L.T., Horne, W.S.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1807301

Revision History  

• Version 1.0: 2023-05-03
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 2.1: 2024-05-01
  Changes: Database references