3RC0

Human SETD6 in complex with RelA Lys310 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling.

Chang, Y.Levy, D.Horton, J.R.Peng, J.Zhang, X.Gozani, O.Cheng, X.

(2011) Nucleic Acids Res. 39: 6380-6389

  • DOI: 10.1093/nar/gkr256
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SET domain containing 6 (SETD6) monomethylates the RelA subunit of nuclear factor kappa B (NF-κB). The ankyrin repeats of G9a-like protein (GLP) recognizes RelA monomethylated at Lys310. Adjacent to Lys310 is Ser311, a known phosphorylation site of R ...

    SET domain containing 6 (SETD6) monomethylates the RelA subunit of nuclear factor kappa B (NF-κB). The ankyrin repeats of G9a-like protein (GLP) recognizes RelA monomethylated at Lys310. Adjacent to Lys310 is Ser311, a known phosphorylation site of RelA. Ser311 phosphorylation inhibits Lys310 methylation by SETD6 as well as binding of Lys310me1 by GLP. The structure of SETD6 in complex with RelA peptide containing the methylation site, in the presence of S-adenosyl-L-methionine, reveals a V-like protein structure and suggests a model for NF-κB binding to SETD6. In addition, structural modeling of the GLP ankyrin repeats bound to Lys310me1 peptide provides insight into the molecular basis for inhibition of Lys310me1 binding by Ser311 phosphorylation. Together, these findings provide a structural explanation for a key cellular signaling pathway centered on RelA Lys310 methylation, which is generated by SETD6 and recognized by GLP, and incorporate a methylation-phosphorylation switch of adjacent lysine and serine residues. Finally, SETD6 is structurally similar to the Rubisco large subunit methyltransferase. Given the restriction of Rubisco to plant species, this particular appearance of the protein lysine methyltransferase has been evolutionarily well conserved.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-lysine methyltransferase SETD6
A, B
449Homo sapiensMutation(s): 0 
Gene Names: SETD6
EC: 2.1.1.-
Find proteins for Q8TBK2 (Homo sapiens)
Go to Gene View: SETD6
Go to UniProtKB:  Q8TBK2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcription factor p65 peptide
P, Q
15Homo sapiensMutation(s): 0 
Gene Names: RELA (NFKB3)
Find proteins for Q04206 (Homo sapiens)
Go to Gene View: RELA
Go to UniProtKB:  Q04206
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.166 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.621α = 78.73
b = 64.501β = 70.60
c = 73.759γ = 64.21
Software Package:
Software NamePurpose
PHENIXrefinement
SGXPROmodel building
HKL-2000data scaling
HKL-2000data collection
SGXPROphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-10
    Type: Database references
  • Version 1.3: 2011-09-07
    Type: Database references