8TW0

Crystal Structure of a synthetic ABC heterotrimeric Collagen-like Peptide at 1.53 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Heterotrimeric collagen helix with high specificity of assembly results in a rapid rate of folding.

Cole, C.C.Walker, D.R.Hulgan, S.A.H.Pogostin, B.H.Swain, J.W.R.Miller, M.D.Xu, W.Duella, R.Misiura, M.Wang, X.Kolomeisky, A.B.Philips Jr., G.N.Hartgerink, J.D.

(2024) Nat Chem 

  • DOI: https://doi.org/10.1038/s41557-024-01573-2
  • Primary Citation of Related Structures:  
    8TW0

  • PubMed Abstract: 

    The most abundant natural collagens form heterotrimeric triple helices. Synthetic mimics of collagen heterotrimers have been found to fold slowly, even compared to the already slow rates of homotrimeric helices. These prolonged folding rates are not understood. Here we compare the stabilities, specificities and folding rates of three heterotrimeric collagen mimics designed through a computationally assisted approach. The crystal structure of one ABC-type heterotrimer verified a well-controlled composition and register and elucidated the geometry of pairwise cation-π and axial and lateral salt bridges in the assembly. This collagen heterotrimer folds much faster (hours versus days) than comparable, well-designed systems. Circular dichroism and NMR data suggest the folding is frustrated by unproductive, competing heterotrimer species and these species must unwind before refolding into the thermodynamically favoured assembly. The heterotrimeric collagen folding rate is inhibited by the introduction of preformed competing triple-helical assemblies, which suggests that slow heterotrimer folding kinetics are dominated by the frustration of the energy landscape caused by competing triple helices.


  • Organizational Affiliation

    Department of Chemistry, Rice University, Houston, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen Mimetic Peptide A31synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen Mimetic Peptide B31synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Collagen Mimetic Peptide C31synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
A
L-PEPTIDE LINKINGC5 H9 N O3PRO
N7P
Query on N7P
A
L-PEPTIDE LINKINGC7 H11 N O3PRO
SAC
Query on SAC
B
L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.706α = 109.42
b = 27.876β = 111.8
c = 28.396γ = 95.73
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Arcimboldophasing
CrysalisProdata scaling
CrysalisProdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE 2203937
National Science Foundation (NSF, United States)United StatesGRFP DGE 1842494
National Science Foundation (NSF, United States)United StatesSTC-1231306
Robert A. Welch FoundationUnited StatesC-2141
Robert A. Welch FoundationUnited StatesC-2118

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Database references