2J3S | pdb_00002j3s

Crystal structure of the human filamin A Ig domains 19 to 21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.297 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.252 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 
    0.257 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2J3S

This is version 1.2 of the entry. See complete history

Literature

Structure of Three Tandem Filamin Domains Reveals Auto-Inhibition of Ligand-Binding.

Lad, Y.Kiema, T.-R.Jiang, P.Pentikanen, O.T.Coles, C.H.Campbell, I.D.Calderwood, D.A.Ylanne, J.

(2007) EMBO J 26: 3993

  • DOI: https://doi.org/10.1038/sj.emboj.7601827
  • Primary Citation Related Structures: 
    2J3S

  • PubMed Abstract: 

    Human filamins are large actin-crosslinking proteins composed of an N-terminal actin-binding domain followed by 24 Ig-like domains (IgFLNs), which interact with numerous transmembrane receptors and cytosolic signaling proteins. Here we report the 2.5 A resolution structure of a three-domain fragment of human filamin A (IgFLNa19-21). The structure reveals an unexpected domain arrangement, with IgFLNa20 partially unfolded bringing IgFLNa21 into close proximity to IgFLNa19. Notably the N-terminus of IgFLNa20 forms a beta-strand that associates with the CD face of IgFLNa21 and occupies the binding site for integrin adhesion receptors. Disruption of this IgFLNa20-IgFLNa21 interaction enhances filamin binding to integrin beta-tails. Structural and functional analysis of other IgFLN domains suggests that auto-inhibition by adjacent IgFLN domains may be a general mechanism controlling filamin-ligand interactions. This can explain the increased integrin binding of filamin splice variants and provides a mechanism by which ligand binding might impact filamin structure.


  • Organizational Affiliation
    • Department of Pharmacology and Interdepartmental Program in Vascular Biology and Transplantation, Yale University School of Medicine, New Haven, CT 06520, USA.

Macromolecule Content 

  • Total Structure Weight: 61.8 kDa 
  • Atom Count: 3,779 
  • Modeled Residue Count: 500 
  • Deposited Residue Count: 576 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FILAMIN-A
A, B
288Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P21333 (Homo sapiens)
Explore P21333 
Go to UniProtKB:  P21333
PHAROS:  P21333
GTEx:  ENSG00000196924 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21333
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DIO

Query on DIO



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
G [auth B],
H [auth B]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
BR

Query on BR



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.297 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.252 (Depositor), 0.248 (DCC) 
  • R-Value Observed: 0.257 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.28α = 90
b = 78.39β = 90
c = 229.04γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description