Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.32 kDa 
• Atom Count: 1260 
• Residue Count: 148 
• Unique protein chains: 1

3TRT

Crystal structure of stabilised vimentin coil2 fragment

• DOI: 10.2210/pdb3TRT/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-09-10 Released: 2012-02-01 
• Deposition Author(s): Chernyatina, A.A., Strelkov, S.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.298 
• R-Value Work: 0.225 
• R-Value Observed: 0.234 

Literature

Stabilization of vimentin coil2 fragment via an engineered disulfide.

Chernyatina, A.A., Strelkov, S.V.

(2012) J Struct Biol 177: 46-53

• PubMed: 22119849 
• DOI: 10.1016/j.jsb.2011.11.014
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vimentin	A, B	77	Homo sapiens	Mutation(s): 3  Gene Names: VIM
Find proteins for P08670 (Homo sapiens) Explore P08670  Go to UniProtKB:  P08670
NIH Common Fund Data Resources
PHAROS  P08670 GTEx  ENSG00000026025

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NH4	A	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 53.419	α = 90
b = 75.521	β = 90
c = 86.859	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHELX	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
go.com	data collection
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-10 
• Released Date: 2012-02-01 
Deposition Author(s): Chernyatina, A.A., Strelkov, S.V.

Revision History 

• 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