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 1.4 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: 10.1093/emboj/21.6.1255
  • Primary Citation of Related Structures:  
    1GK4, 1GK7, 1GK6

  • 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 ...

    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.


    Related Citations: 
    • Divide-and-Conquer Crystallographic Approach Towards an Atomic Structure of Intermediate Filaments
      Strelkov, S.V., Herrmann, H., Geisler, N., Lustig, A., Ivaninskii, S., Zimbelmann, R., Burkhard, P., Aebi, U.
      (2001) J Mol Biol 306: 773
    • The Intermediate Filament Protein Consensus Motifof Helix 2B: Its Atomic Structure and Contribution to Assembly
      Herrmann, H., Strelkov, S.V., Feja, B., Rogers, K.R., Brettel, M., Lustig, A., Haener, M., Parry, D.A.D., Steinert, P.M., Burkhard, P., Aebi, U.
      (2000) J Mol Biol 298: 817

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VIMENTINAB59Saccharomyces cerevisiaeHomo sapiens
This entity is chimeric
Mutation(s): 0 
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
NIH Common Fund Data Resources
PHAROS  P08670
Protein Feature View
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  • 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 

  • 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