3R6N

Crystal structure of a rigid four spectrin repeat fragment of the human desmoplakin plakin domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a rigid four-spectrin-repeat fragment of the human desmoplakin plakin domain.

Choi, H.J.Weis, W.I.

(2011) J.Mol.Biol. 409: 800-812

  • DOI: 10.1016/j.jmb.2011.04.046

  • PubMed Abstract: 
  • The plakin protein family serves to connect cell-cell and cell-matrix adhesion molecules to the intermediate filament cytoskeleton. Desmoplakin (DP) is an integral part of desmosomes, where it links desmosomal cadherins to the intermediate filaments. ...

    The plakin protein family serves to connect cell-cell and cell-matrix adhesion molecules to the intermediate filament cytoskeleton. Desmoplakin (DP) is an integral part of desmosomes, where it links desmosomal cadherins to the intermediate filaments. The 1056-amino-acid N-terminal region of DP contains a plakin domain common to members of the plakin family. Plakin domains contain multiple copies of spectrin repeats (SRs). We determined the crystal structure of a fragment of DP, residues 175-630, consisting of four SRs and an inserted SH3 domain. The four repeats form an elongated, rigid structure. The SH3 domain is present in a loop between two helices of an SR and interacts extensively with the preceding SR in a manner that appears to limit inter-repeat flexibility. The intimate intramolecular association of the SH3 domain with the preceding SR is also observed in plectin, another plakin protein, but not in α-spectrin, suggesting that the SH3 domain of plakins contributes to the stability and rigidity of this subfamily of SR-containing proteins.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Desmoplakin
A, B
450Homo sapiensMutation(s): 0 
Gene Names: DSP
Find proteins for P15924 (Homo sapiens)
Go to Gene View: DSP
Go to UniProtKB:  P15924
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D1D
Query on D1D

Download SDF File 
Download CCD File 
A, B
(4S,5S)-1,2-DITHIANE-4,5-DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-QWWZWVQMSA-N
 Ligand Interaction
DTT
Query on DTT

Download SDF File 
Download CCD File 
A, B
2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 157.520α = 90.00
b = 82.520β = 125.54
c = 139.980γ = 90.00
Software Package:
Software NamePurpose
RESOLVEphasing
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing
SCALAdata scaling
PDB_EXTRACTdata extraction
SnBphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance