7JX4 | pdb_00007jx4

Crystal Structure of N-Lysine Peptoid-modified Collagen Triple Helix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 
    0.158 (Depositor), 0.158 (DCC) 
  • R-Value Work: 
    0.140 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.141 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7JX4

This is version 2.0 of the entry. See complete history

Literature

Peptoid Residues Make Diverse, Hyperstable Collagen Triple-Helices.

Kessler, J.L.Kang, G.Qin, Z.Kang, H.Whitby, F.G.Cheatham, T.E.Hill, C.P.Li, Y.Yu, S.M.

(2021) J Am Chem Soc 143: 10910-10919

  • DOI: https://doi.org/10.1021/jacs.1c00708
  • Primary Citation Related Structures: 
    7JX4, 7JX5

  • PubMed Abstract: 

    As the only ribosomally encoded N-substituted amino acid, proline promotes distinct secondary protein structures. The high proline content in collagen, the most abundant protein in the human body, is crucial to forming its hallmark structure: the triple-helix. For over five decades, proline has been considered compulsory for synthetic designs aimed at recapitulating collagen's structure and properties. Here we describe that N-substituted glycines (N-glys), also known as peptoid residues, exhibit a general triple-helical propensity similar to or greater than proline, enabling synthesis of stable triple-helical collagen mimetic peptides (CMPs) with unprecedented side chain diversity. Supported by atomic-resolution crystal structures as well as circular dichroism and computational characterizations spanning over 30 N-gly-containing CMPs, we discovered that N-glys stabilize the triple-helix primarily by sterically preorganizing individual chains into the polyproline-II helix. We demonstrated that N-glys with exotic side chains including a "click"-able alkyne and a photosensitive side chain enable CMPs for functional applications including the spatiotemporal control of cell adhesion and migration. The structural principles uncovered in this study open up opportunities for a new generation of collagen-mimetic therapeutics and materials.


  • Organizational Affiliation
    • Department of Biomedical Engineering, University of Utah, Salt Lake City, Utah 84112, United States.

Macromolecule Content 

  • Total Structure Weight: 5.83 kDa 
  • Atom Count: 532 
  • Modeled Residue Count: 69 
  • Deposited Residue Count: 69 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen mimetic peptide with N-Lysine guest
A, B, C
23Homo sapiensMutation(s): 0 

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HYP
Query on HYP
A, B, C
L-PEPTIDE LINKINGC5 H9 N O3PRO
NLY
Query on NLY
A, B, C
PEPTIDE LINKINGC6 H14 N2 O2GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free:  0.158 (Depositor), 0.158 (DCC) 
  • R-Value Work:  0.140 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.141 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.365α = 90
b = 24.756β = 98.72
c = 25.357γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01AR071358

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2021-08-11
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations