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 
  • R-Value Observed: 0.169 

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Ligand Structure Quality Assessment 


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:  
    3QXY, 3RC0

  • 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 RelA. Ser311 phosphorylation inhibits Lys310 methylation by SETD6 as well as binding of Lys310me1 by GLP ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
N-lysine methyltransferase SETD6A, C [auth B]449Homo sapiensMutation(s): 0 
Gene Names: SETD6
EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBK2 (Homo sapiens)
Explore Q8TBK2 
Go to UniProtKB:  Q8TBK2
PHAROS:  Q8TBK2
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor p65 peptideB [auth P], D [auth Q]15Homo sapiensMutation(s): 0 
Gene Names: RELANFKB3
UniProt & NIH Common Fund Data Resources
Find proteins for Q04206 (Homo sapiens)
Explore Q04206 
Go to UniProtKB:  Q04206
PHAROS:  Q04206
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAM (Subject of Investigation/LOI)
Query on SAM

Download Ideal Coordinates CCD File 
O [auth A], V [auth B]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  P [auth B],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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 
  • R-Value Observed: 0.169 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.621α = 78.73
b = 64.501β = 70.6
c = 73.759γ = 64.21
Software Package:
Software NamePurpose
HKL-2000data collection
SGXPROmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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