4DAT

Structure of 14-3-3 sigma in complex with PADI6 14-3-3 binding motif II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification and structural characterization of two 14-3-3 binding sites in the human peptidylarginine deiminase type VI.

Rose, R.Rose, M.Ottmann, C.

(2012) J.Struct.Biol. 180: 65-72

  • DOI: 10.1016/j.jsb.2012.05.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The regulation and function of peptidylarginine deiminase isoform VI (PAD6), which is a highly abundant protein associated with the cytoplasmic lattices in mammalian oocytes, is poorly understood so far. It has been shown previously, that 14-3-3 prot ...

    The regulation and function of peptidylarginine deiminase isoform VI (PAD6), which is a highly abundant protein associated with the cytoplasmic lattices in mammalian oocytes, is poorly understood so far. It has been shown previously, that 14-3-3 proteins, a class of regulatory adapter proteins ubiquitous in eukaryotes, bind to PAD6 in vivo in a phosphorylation dependent manner. Here we identify possible 14-3-3 binding sites in human PAD6 by in silico methods, looking for conserved, surface exposed serine residues. Two of these sites were confirmed as 14-3-3 binding sites by fluorescence polarization competition and X-ray crystallography. We furthermore suggest a role of RSK-type kinases in the phosphorylation of one of these two binding sites and provide evidence in the form of in vitro kinase assays with p70S6 kinase and RSK1.


    Organizational Affiliation

    Chemical Genomics Centre of the Max-Planck-Society, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
14-3-3 protein sigma
A
234Homo sapiensMutation(s): 0 
Gene Names: SFN (HME1)
Find proteins for P31947 (Homo sapiens)
Go to Gene View: SFN
Go to UniProtKB:  P31947
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptidylarginine Deiminase type VI
B
9Homo sapiensMutation(s): 0 
Gene Names: PADI6 (PAD6)
EC: 3.5.3.15
Find proteins for Q6TGC4 (Homo sapiens)
Go to Gene View: PADI6
Go to UniProtKB:  Q6TGC4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.147 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.220α = 90.00
b = 112.360β = 90.00
c = 62.730γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
go.comdata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2012-10-24
    Type: Database references