5DCP

Crystal structure of the human filamin B Ig-like domains 16-17


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Skeletal Dysplasia Mutations Effect on Human Filamins' Structure and Mechanosensing.

Seppala, J.Bernardi, R.C.Haataja, T.J.K.Hellman, M.Pentikainen, O.T.Schulten, K.Permi, P.Ylanne, J.Pentikainen, U.

(2017) Sci Rep 7: 4218-4218

  • DOI: https://doi.org/10.1038/s41598-017-04441-x
  • Primary Citation of Related Structures:  
    5DCP

  • PubMed Abstract: 

    Cells' ability to sense mechanical cues in their environment is crucial for fundamental cellular processes, leading defects in mechanosensing to be linked to many diseases. The actin cross-linking protein Filamin has an important role in the conversion of mechanical forces into biochemical signals. Here, we reveal how mutations in Filamin genes known to cause Larsen syndrome and Frontometaphyseal dysplasia can affect the structure and therefore function of Filamin domains 16 and 17. Employing X-ray crystallography, the structure of these domains was first solved for the human Filamin B. The interaction seen between domains 16 and 17 is broken by shear force as revealed by steered molecular dynamics simulations. The effects of skeletal dysplasia associated mutations of the structure and mechanosensing properties of Filamin were studied by combining various experimental and theoretical techniques. The results showed that Larsen syndrome associated mutations destabilize or even unfold domain 17. Interestingly, those Filamin functions that are mediated via domain 17 interactions with other proteins are not necessarily affected as strongly interacting peptide binding to mutated domain 17 induces at least partial domain folding. Mutation associated to Frontometaphyseal dysplasia, in turn, transforms 16-17 fragment from compact to an elongated form destroying the force-regulated domain pair.


  • Organizational Affiliation

    Department of Biological and Environmental Science and Nanoscience Center, University of Jyvaskyla, P.O Box 35, Survontie 9 C, FI-40014, Jyvaskyla, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Filamin-B
A, B
175Homo sapiensMutation(s): 0 
Gene Names: FLNBFLN1LFLN3TABPTAP
UniProt & NIH Common Fund Data Resources
Find proteins for O75369 (Homo sapiens)
Explore O75369 
Go to UniProtKB:  O75369
PHAROS:  O75369
GTEx:  ENSG00000136068 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75369
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.62α = 90
b = 80.62β = 90
c = 118.016γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2018-04-11
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description