3TRT | pdb_00003trt

Crystal structure of stabilised vimentin coil2 fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.298 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3TRT

This is version 1.3 of the entry. See complete history

Literature

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 Related Structures: 
    3TRT

  • 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.

Macromolecule Content 

  • Total Structure Weight: 18.32 kDa 
  • Atom Count: 1,260 
  • Modeled Residue Count: 148 
  • Deposited Residue Count: 154 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vimentin
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
PHAROS:  P08670
GTEx:  ENSG00000026025 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08670
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
G [auth B],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NH4

Query on NH4



Download:Ideal Coordinates CCD File
F [auth A]AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.298 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
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
SHELXphasing
SHELXmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
go.comdata collection
SHELXCDphasing
SHELXEmodel building

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary