4DAT | pdb_00004dat

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

• PDB DOI: https://doi.org/10.2210/pdb4DAT/pdb

• Classification: SIGNALING PROTEIN/PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-13 Released: 2012-06-13 
• Deposition Author(s): Rose, R., Rose, M., Ottmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.183 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

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

• PubMed: 22634725 
• DOI: https://doi.org/10.1016/j.jsb.2012.05.010
• Primary Citation 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 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.

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Organizational Affiliation: 
• Chemical Genomics Centre of the Max-Planck-Society, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.46 kDa 
• Atom Count: 2,337 
• Modeled Residue Count: 227 
• Deposited Residue Count: 243 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein sigma	A	234	Homo sapiens	Mutation(s): 0  Gene Names: SFN, HME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens) Explore P31947  Go to UniProtKB:  P31947
PHAROS:  P31947 GTEx:  ENSG00000175793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidylarginine Deiminase type VI	B	9	Homo sapiens	Mutation(s): 0  EC: 3.5.3.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q6TGC4 (Homo sapiens) Explore Q6TGC4  Go to UniProtKB:  Q6TGC4
PHAROS:  Q6TGC4 GTEx:  ENSG00000276747

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.183 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.22	α = 90
b = 112.36	β = 90
c = 62.73	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
go.com	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Rose, R., Rose, M., Ottmann, C.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2012-10-24
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary