6SNK

Crystal structure of the Collagen VI alpha3 N2 domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure of a collagen VI alpha 3 chain VWA domain array: adaptability and functional implications of myopathy causing mutations.

Solomon-Degefa, H., Gebauer, J.M., Jeffries, C.M., Freiburg, C.D., Meckelburg, P., Bird, L.E., Baumann, U., Svergun, D.I., Owens, R.J., Werner, J.M., Behrmann, E., Paulsson, M., Wagener, R.

(2020) J Biol Chem 295: 12755-12771

  • DOI: 10.1074/jbc.RA120.014865
  • Primary Citation of Related Structures:  
    6SNK

  • PubMed Abstract: 

    • Collagen VI is a ubiquitous heterotrimeric protein of the extracellular matrix (ECM) that plays an essential role in the proper maintenance of skeletal muscle. Mutations in collagen VI lead to a spectrum of congenital myopathies, from the mild Bethlem myopathy to the severe Ullrich congenital muscular dystrophy ...

    Collagen VI is a ubiquitous heterotrimeric protein of the extracellular matrix (ECM) that plays an essential role in the proper maintenance of skeletal muscle. Mutations in collagen VI lead to a spectrum of congenital myopathies, from the mild Bethlem myopathy to the severe Ullrich congenital muscular dystrophy. Collagen VI contains only a short triple helix and consists primarily of von Willebrand factor type A (VWA) domains, protein-protein interaction modules found in a range of ECM proteins. Disease-causing mutations occur commonly in the VWA domains, and the second VWA domain of the α3 chain, the N2 domain, harbors several such mutations. Here, we investigate structure-function relationships of the N2 mutations to shed light on their possible myopathy mechanisms. We determined the X-ray crystal structure of N2, combined with monitoring secretion efficiency in cell culture of selected N2 single-domain mutants, finding that mutations located within the central core of the domain severely affect secretion efficiency. In longer α3 chain constructs, spanning N6-N3, small-angle X-ray scattering demonstrates that the tandem VWA array has a modular architecture and samples multiple conformations in solution. Single-particle EM confirmed the presence of multiple conformations. Structural adaptability appears intrinsic to the VWA domain region of collagen VI α3 and has implications for binding interactions and modulating stiffness within the ECM.

    Organizational Affiliation: 

    Cologne Center for Musculoskeletal Biomechanics (CCMB), Cologne, Germany.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Collagen alpha-3(VI) chainA, B200Homo sapiensMutation(s): 0 
Gene Names: COL6A3
UniProt & NIH Common Fund Data Resources
Find proteins for P12111 (Homo sapiens)
Explore P12111 
Go to UniProtKB:  P12111
PHAROS:  P12111
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12111
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.639α = 83.342
b = 40.538β = 76.792
c = 57.114γ = 79.559
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB829 / B11
German Research FoundationGermanyINST 216/682-1

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2020-09-16
    Changes: Database references