6SYJ | pdb_00006syj

Crystal structure of a ProM2 containing triple-helical collagen peptide.

• PDB DOI: https://doi.org/10.2210/pdb6SYJ/pdb

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


• Deposited: 2019-09-30 Released: 2020-01-29 
• Deposition Author(s): Gebauer, J.M., Maassen, A., Schmalz, H.-G., Baumann, U.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.81 Å
• R-Value Free: 
  0.136 (Depositor), 0.136 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.128 (DCC) 

Starting Model: experimental

Literature

Triple-Helix-Stabilizing Effects in Collagen Model Peptides Containing PPII-Helix-Preorganized Diproline Modules.

Maassen, A., Gebauer, J.M., Theres Abraham, E., Grimm, I., Neudorfl, J.M., Kuhne, R., Neundorf, I., Baumann, U., Schmalz, H.G.

(2020) Angew Chem Int Ed Engl 59: 5747-5755

• PubMed: 31944532 
• DOI: https://doi.org/10.1002/anie.201914101
• Primary Citation Related Structures: 
  6SYJ


• PubMed Abstract: 
  

  Collagen model peptides (CMPs) serve as tools for understanding stability and function of the collagen triple helix and have a potential for biomedical applications. In the past, interstrand cross-linking or conformational preconditioning of proline units through stereoelectronic effects have been utilized in the design of stabilized CMPs. To further study the effects determining collagen triple helix stability we investigated a series of CMPs containing synthetic diproline-mimicking modules (ProMs), which were preorganized in a PPII-helix-type conformation by a functionalizable intrastrand C ₂ bridge. Results of CD-based denaturation studies were correlated with calculated (DFT) conformational preferences of the ProM units, revealing that the relative helix stability is mainly governed by an interplay of main-chain preorganization, ring-flip preference, adaptability, and steric effects. Triple helix integrity was proven by crystal structure analysis and binding to HSP47.

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Organizational Affiliation: 
• University of Cologne, Department of Chemistry, Greinstraße 4, 50939, Cologne, Germany.
University of Cologne, Department of Chemistry, Zülpicher Straße 47a, 50674, Cologne, Germany.
Leibniz-Institut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Rössle-Straße 10, 13125, Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 8.68 kDa 
• Atom Count: 842 
• Modeled Residue Count: 93 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ProM2 containing collagen model peptide.	A, B, C	33	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.81 Å
• R-Value Free:  0.136 (Depositor), 0.136 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.128 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.08	α = 90
b = 22.85	β = 103.83
c = 53.43	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Gebauer, J.M., Maassen, A., Schmalz, H.-G., Baumann, U.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	INST 216/682-1

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2020-02-12
  Changes: Database references
• Version 1.2: 2020-04-01
  Changes: Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-01-24
  Changes: Refinement description
• Version 2.2: 2024-10-09
  Changes: Structure summary