3KLT

Crystal structure of a vimentin fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.293 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Atomic structure of vimentin coil 2.

Nicolet, S.Herrmann, H.Aebi, U.Strelkov, S.V.

(2010) J Struct Biol 170: 369-376

  • DOI: 10.1016/j.jsb.2010.02.012
  • Primary Citation of Related Structures:  
    3KLT

  • PubMed Abstract: 
  • Intermediate filaments (IFs) are essential cytoskeletal components in metazoan cells. They assemble from elementary dimers that are built around the central alpha-helical coiled-coil rod domain representing the IF 'signature'. The rod consists of two similarly-sized parts, coil 1 and coil 2, connected by a non-alpha-helical linker L12 ...

    Intermediate filaments (IFs) are essential cytoskeletal components in metazoan cells. They assemble from elementary dimers that are built around the central alpha-helical coiled-coil rod domain representing the IF 'signature'. The rod consists of two similarly-sized parts, coil 1 and coil 2, connected by a non-alpha-helical linker L12. Coil 2 is absolutely conserved in length across all IF types and was initially predicted to consist of a short coiled-coil segment 2A based on a heptad pattern of hydrophobic residues, another linker L2 and a coiled-coil segment 2B. Here we present the crystal structure of human vimentin fragment including residues 261-335 i.e. approximately the first half of coil 2. The N-terminal part of this fragment reveals a parallel alpha-helical bundle characterized by 3.5 consecutive hendecad repeats. It is immediately followed by a regular left-handed coiled coil. The distinct non-helical linker L2 is therefore not observed. Together with the previously determined crystal structure of the major part of segment 2B (Strelkov et al., 2002), we can now build a complete atomic model of the 21nm long vimentin coil 2 dimer being a relatively rigid rod.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, Katholieke Universiteit Leuven, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VimentinA, B, C, D72Homo sapiensMutation(s): 0 
Gene Names: VIM
Find proteins for P08670 (Homo sapiens)
Explore P08670 
Go to UniProtKB:  P08670
NIH Common Fund Data Resources
PHAROS:  P08670
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33

Download Ideal Coordinates CCD File 
E [auth A]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download Ideal Coordinates CCD File 
G [auth B]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

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N [auth D]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
K [auth C], L [auth C]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
SM
Query on SM

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F [auth A], H [auth B], P [auth D]SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
O [auth D]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
I [auth B], J [auth B], M [auth C], Q [auth D], R [auth D], S [auth D]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.293 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.2α = 90
b = 30.1β = 102.71
c = 82.98γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
SHARPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance