8TW0 | pdb_00008tw0

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

• PDB DOI: https://doi.org/10.2210/pdb8TW0/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2023-08-18 Released: 2024-05-29 
• Deposition Author(s): Miller, M.D., Cole, C.C., Xu, W., Walker, D.R., Hulgan, S.A.H., Pogostin, B.H., Swain, J.W.R., Duella, R., Misiura, M., Wang, X., Kolomeisky, A.B., Phillips Jr., G.N., Hartgerink, J.D.
• Funding Organization(s): National Science Foundation (NSF, United States), Robert A. Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.185 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

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 16: 1698-1704

• PubMed: 39009792 
• DOI: https://doi.org/10.1038/s41557-024-01573-2
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Rice University, Houston, TX, USA.
Department of Bioengineering, Rice University, Houston, TX, USA.
Department of Biosciences, Rice University, Houston, TX, USA.
Shared Equipment Authority, Rice University, Houston, TX, USA.
Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
Department of Physics and Astronomy, Rice University, Houston, TX, USA.
Department of Chemistry, Rice University, Houston, TX, USA. [e-mail].
Department of Bioengineering, Rice University, Houston, TX, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: assay for oligomerization, NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 9.38 kDa 
• Atom Count: 852 
• Modeled Residue Count: 93 
• Deposited Residue Count: 96 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen Mimetic Peptide A	A	32	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen Mimetic Peptide B	B	32	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen Mimetic Peptide C	C	32	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth C], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	A	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.185 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.706	α = 109.42
b = 27.876	β = 111.8
c = 28.396	γ = 95.73

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
Arcimboldo	phasing
CrysalisPro	data scaling
CrysalisPro	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Miller, M.D., Cole, C.C., Xu, W., Walker, D.R., Hulgan, S.A.H., Pogostin, B.H., Swain, J.W.R., Duella, R., Misiura, M., Wang, X., Kolomeisky, A.B., Phillips Jr., G.N., Hartgerink, J.D.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE 2203937
National Science Foundation (NSF, United States)	United States	GRFP DGE 1842494
National Science Foundation (NSF, United States)	United States	STC-1231306
Robert A. Welch Foundation	United States	C-2141
Robert A. Welch Foundation	United States	C-2118

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release
  
• Version 1.1: 2024-07-31
  Changes: Database references
• Version 2.0: 2024-10-16
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary