Crystal structure of stabilised vimentin coil2 fragment

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.234 

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Stabilization of vimentin coil2 fragment via an engineered disulfide.

Chernyatina, A.A.Strelkov, S.V.

(2012) J Struct Biol 177: 46-53

  • DOI: https://doi.org/10.1016/j.jsb.2011.11.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Cytoskeletal intermediate filaments (IFs) assemble from the elementary dimers based on a segmented α-helical coiled-coil (CC) structure. Crystallographic studies of IF protein fragments remain the main route to access their atomic structure. To enable crystallization, such fragments must be sufficiently short. As a consequence, they often fail to assemble into the correct CC dimers. In particular, human vimentin fragment D3 corresponding to the first half of coil2 (residues 261-335) stays monomeric in solution. We have induced its dimerization via introducing a disulfide link between two cysteines engineered in the hydrophobic core of the CC close to its N-terminus. The 2.3 Å crystal structure of the D3st (stabilized) fragment reveals a mostly parallel α-helical bundle structure in its N-terminal half which smoothly continues into a left-handed CC towards the C-terminus. This provides a direct evidence for a continuously α-helical structure of the coil2 segment and disproves the previously suggested existence of linker L2 separating it into two left-handed CCs. The general principles of CC dimer stabilization by disulfide introduction are also discussed.

  • Organizational Affiliation

    Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
77Homo sapiensMutation(s): 3 
Gene Names: VIM
UniProt & NIH Common Fund Data Resources
Find proteins for P08670 (Homo sapiens)
Explore P08670 
Go to UniProtKB:  P08670
GTEx:  ENSG00000026025 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08670
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.234 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.419α = 90
b = 75.521β = 90
c = 86.859γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
PDB_EXTRACTdata extraction
go.comdata collection
SHELXEmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-01
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2018-06-06
    Changes: Data collection, Refinement description