4IGI

Crystal structure of the Collagen VI alpha3 N5 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.120 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A structure of a collagen VI VWA domain displays N and C termini at opposite sides of the protein

Becker, A.K.Mikolajek, H.Paulsson, M.Wagener, R.Werner, J.M.

(2014) Structure 22: 199-208

  • DOI: 10.1016/j.str.2013.06.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Von Willebrand factor A (VWA) domains are versatile protein interaction domains with N and C termini in close proximity placing spatial constraints on overall protein structure. The 1.2 Å crystal structures of a collagen VI VWA domain and a disease-c ...

    Von Willebrand factor A (VWA) domains are versatile protein interaction domains with N and C termini in close proximity placing spatial constraints on overall protein structure. The 1.2 Å crystal structures of a collagen VI VWA domain and a disease-causing point mutant show C-terminal extensions that place the N and C termini at opposite ends. This allows a "beads-on-a-string" arrangement of multiple VWA domains as observed for ten N-terminal domains of the collagen VI α3 chain. The extension is linked to the core domain by a salt bridge and two hydrophobic patches. Comparison of the wild-type and a muscular dystrophy-associated mutant structure identifies a potential perturbation of a protein interaction interface and indeed, the secretion of mutant collagen VI tetramers is affected. Homology modeling is used to locate a number of disease-associated mutations and analyze their structural impact, which will allow mechanistic analysis of collagen-VI-associated muscular dystrophy phenotypes.


    Organizational Affiliation

    Center for Biochemistry, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany. Electronic address: raimund.wagener@uni-koeln.de.,Centre for Biological Sciences, B85 Life Sciences Building M55, University of Southampton, Southampton SO17 1BJ, UK.,Centre for Biological Sciences, B85 Life Sciences Building M55, University of Southampton, Southampton SO17 1BJ, UK. Electronic address: j.m.werner@soton.ac.uk.,Center for Biochemistry, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Collagen alpha3(VI)
A
203Mus musculusMutation(s): 0 
Gene Names: Col6a3
Find proteins for E9PWQ3 (Mus musculus)
Go to UniProtKB:  E9PWQ3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.120 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.730α = 90.00
b = 58.460β = 112.97
c = 39.160γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHENIXrefinement
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2018-12-05
    Type: Data collection, Database references