3G1E

X-ray crystal structure of coil 1A of human vimentin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Vimentin coil 1A-A molecular switch involved in the initiation of filament elongation.

Meier, M.Padilla, G.P.Herrmann, H.Wedig, T.Hergt, M.Patel, T.R.Stetefeld, J.Aebi, U.Burkhard, P.

(2009) J.Mol.Biol. 390: 245-261

  • DOI: 10.1016/j.jmb.2009.04.067

  • PubMed Abstract: 
  • Interestingly, our previously published structure of the coil 1A fragment of the human intermediate filament protein vimentin turned out to be a monomeric alpha-helical coil instead of the expected dimeric coiled coil. However, the 39-amino-acid-long ...

    Interestingly, our previously published structure of the coil 1A fragment of the human intermediate filament protein vimentin turned out to be a monomeric alpha-helical coil instead of the expected dimeric coiled coil. However, the 39-amino-acid-long helix had an intrinsic curvature compatible with a coiled coil. We have now designed four mutants of vimentin coil 1A, modifying key a and d positions in the heptad repeat pattern, with the aim of investigating the molecular criteria that are needed to stabilize a dimeric coiled-coil structure. We have analysed the biophysical properties of the mutants by circular dichroism spectroscopy, analytical ultracentrifugation and X-ray crystallography. All four mutants exhibited an increased stability over the wild type as indicated by a rise in the melting temperature (T(m)). At a concentration of 0.1 mg/ml, the T(m) of the peptide with the single point mutation Y117L increased dramatically by 46 degrees C compared with the wild-type peptide. In general, the introduction of a single stabilizing point mutation at an a or a d position did induce the formation of a stable dimer as demonstrated by sedimentation equilibrium experiments. The dimeric oligomerisation state of the Y117L peptide was furthermore confirmed by X-ray crystallography, which yielded a structure with a genuine coiled-coil geometry. Most notably, when this mutation was introduced into full-length vimentin, filament assembly was completely arrested at the unit-length filament (ULF) level, both in vitro and in cDNA-transfected cultured cells. Therefore, the low propensity of the wild-type coil 1A to form a stable two-stranded coiled coil is most likely a prerequisite for the end-to-end annealing of ULFs into filaments. Accordingly, the coil 1A domains might "switch" from a dimeric alpha-helical coiled coil into a more open structure, thus mediating, within the ULFs, the conformational rearrangements of the tetrameric subunits that are needed for the intermediate filament elongation reaction.


    Related Citations: 
    • Near-UV Circular Dichroism Reveals Structural Transitions of Vimentin Subunits during Intermediate Filament Assembly
      Georgakopoulou, S.,Moeller, D.,Sachs, N.,Herrmann, H.,Aebi, U.
      (2009) J.Mol.Biol. 386: 544


    Organizational Affiliation

    Department of Chemistry, University of Manitoba, Winnipeg, Canada. meier@cc.umanitoba.ca




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vimentin
A, B
39Homo sapiensMutation(s): 1 
Gene Names: VIM
Find proteins for P08670 (Homo sapiens)
Go to Gene View: VIM
Go to UniProtKB:  P08670
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
A, B
NON-POLYMERH2 N

--

ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.253 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 35.496α = 90.00
b = 35.496β = 90.00
c = 108.022γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
CrysalisProdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description