5L0C

Human metavinculin (residues 959-1134) in complex with PIP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Differential lipid binding of vinculin isoforms promotes quasi-equivalent dimerization.

Chinthalapudi, K.Rangarajan, E.S.Brown, D.T.Izard, T.

(2016) Proc.Natl.Acad.Sci.USA 113: 9539-9544

  • DOI: 10.1073/pnas.1600702113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The main cause of death globally remains debilitating heart conditions, such as dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), which are often due to mutations of specific components of adhesion complexes. Vinculin regulates thes ...

    The main cause of death globally remains debilitating heart conditions, such as dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), which are often due to mutations of specific components of adhesion complexes. Vinculin regulates these complexes and plays essential roles in intercalated discs that are necessary for muscle cell function and coordinated movement and in the development and function of the heart. Humans bearing familial or sporadic mutations in vinculin suffer from chronic, progressively debilitating DCM that ultimately leads to cardiac failure and death, whereas autosomal dominant mutations in vinculin can also provoke HCM, causing acute cardiac failure. The DCM/HCM-associated mutants of vinculin occur in the 68-residue insert unique to the muscle-specific, alternatively spliced isoform of vinculin, termed metavinculin (MV). Contrary to studies that suggested that phosphoinositol-4,5-bisphosphate (PIP2) only induces vinculin homodimers, which are asymmetric, we show that phospholipid binding results in a domain-swapped symmetric MV dimer via a quasi-equivalent interface compared with vinculin involving R975. Although one of the two PIP2 binding sites is preserved, the symmetric MV dimer that bridges two PIP2 molecules differs from the asymmetric vinculin dimer that bridges only one PIP2 Unlike vinculin, wild-type MV and the DCM/HCM-associated R975W mutant bind PIP2 in their inactive conformations, and R975W MV fails to dimerize. Mutating selective vinculin residues to their corresponding MV residues, or vice versa, switches the isoform's dimeric constellation and lipid binding site. Collectively, our data suggest that MV homodimerization modulates microfilament attachment at muscular adhesion sites and furthers our understanding of MV-mediated cardiac remodeling.


    Organizational Affiliation

    Cell Adhesion Laboratory, Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458; Department of Immunology and Microbial Sciences, The Scripps Research Institute, Jupiter, FL 33458;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vinculin
A, B, C, D
176Homo sapiensMutation(s): 0 
Gene Names: VCL
Find proteins for P18206 (Homo sapiens)
Go to Gene View: VCL
Go to UniProtKB:  P18206
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
PIO
Query on PIO

Download SDF File 
Download CCD File 
A, B, C, D
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.235 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/559 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 114.520α = 90.00
b = 100.676β = 122.49
c = 105.615γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-07
    Type: Database references
  • Version 1.2: 2017-11-01
    Type: Author supporting evidence, Database references, Derived calculations