1GK6

Human vimentin coil 2B fragment linked to GCN4 leucine zipper (Z2B)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Conserved Segments 1A and 2B of the Intermediate Filament Dimer: Their Atomic Structures and Role in Filament Assembly.

Strelkov, S.Herrmann, H.Geisler, N.Wedig, T.Zimbelmann, R.Aebi, U.Burkhard, P.

(2002) EMBO J 21: 1255

  • DOI: https://doi.org/10.1093/emboj/21.6.1255
  • Primary Citation of Related Structures:  
    1GK4, 1GK6, 1GK7

  • PubMed Abstract: 

    Intermediate filaments (IFs) are key components of the cytoskeleton in higher eukaryotic cells. The elementary IF 'building block' is an elongated coiled-coil dimer consisting of four consecutive alpha-helical segments. The segments 1A and 2B include highly conserved sequences and are critically involved in IF assembly. Based on the crystal structures of three human vimentin fragments at 1.4-2.3 A resolution (PDB entries 1gk4, 1gk6 and 1gk7), we have established the molecular organization of these two segments. The fragment corresponding to segment 1A forms a single, amphipatic alpha-helix, which is compatible with a coiled-coil geometry. While this segment might yield a coiled coil within an isolated dimer, monomeric 1A helices are likely to play a role in specific dimer-dimer interactions during IF assembly. The 2B segment reveals a double-stranded coiled coil, which unwinds near residue Phe351 to accommodate a 'stutter'. A fragment containing the last seven heptads of 2B interferes heavily with IF assembly and also transforms mature vimentin filaments into a new kind of structure. These results provide the first insight into the architecture and functioning of IFs at the atomic level.


  • Organizational Affiliation

    Maurice E.Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland. sergei-v.strelkov@unibas.ch


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VIMENTIN
A, B
59Saccharomyces cerevisiaeHomo sapiens
This entity is chimeric
Mutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03069 
Go to UniProtKB:  P03069
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 GroupsP08670P03069
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.801α = 90
b = 98.801β = 90
c = 36.473γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-15
    Type: Initial release
  • Version 1.1: 2015-11-25
    Changes: Data collection, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2017-03-15
    Changes: Source and taxonomy
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-07-24
    Changes: Data collection
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description