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: 1.40 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 

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:  
    4DAT, 4DAU

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
14-3-3 protein sigmaA234Homo sapiensMutation(s): 0 
Gene Names: SFNHME1
Find proteins for P31947 (Homo sapiens)
Explore P31947 
Go to UniProtKB:  P31947
NIH Common Fund Data Resources
PHAROS  P31947
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidylarginine Deiminase type VIB9Homo sapiensMutation(s): 0 
Gene Names: PADI6PAD6
EC: 3.5.3.15
Find proteins for Q6TGC4 (Homo sapiens)
Explore Q6TGC4 
Go to UniProtKB:  Q6TGC4
NIH Common Fund Data Resources
PHAROS  Q6TGC4
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.149 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.22α = 90
b = 112.36β = 90
c = 62.73γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
go.comdata collection
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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