8RVE | pdb_00008rve

Vimentin intermediate filament


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8RVE

This is version 1.3 of the entry. See complete history

Literature

Vimentin filaments integrate low-complexity domains in a complex helical structure.

Eibauer, M.Weber, M.S.Kronenberg-Tenga, R.Beales, C.T.Boujemaa-Paterski, R.Turgay, Y.Sivagurunathan, S.Kraxner, J.Koster, S.Goldman, R.D.Medalia, O.

(2024) Nat Struct Mol Biol 31: 939-949

  • DOI: https://doi.org/10.1038/s41594-024-01261-2
  • Primary Citation Related Structures: 
    8RVE

  • PubMed Abstract: 

    Intermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion-beam milling, cryo-electron microscopy and tomography to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, intertwined and flexible helical structure of 40 α-helices in cross-section, organized into five protofibrils. Surprisingly, the intrinsically disordered head domains form a fiber in the lumen of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking mechanical strength and stretchability.


  • Organizational Affiliation
    • Department of Biochemistry, University of Zurich, Zurich, Switzerland. m.eibauer@bioc.uzh.ch.

Macromolecule Content 

  • Total Structure Weight: 4,190.36 kDa 
  • Atom Count: 54,788 
  • Modeled Residue Count: 13,697 
  • Deposited Residue Count: 36,348 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vimentin466Homo sapiensMutation(s): 0 
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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_207453

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Database references
  • Version 1.2: 2024-07-03
    Changes: Database references
  • Version 1.3: 2024-11-06
    Changes: Structure summary