5HQ2

Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.397 
  • R-Value Work: 0.339 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate.

Girish, T.S.McGinty, R.K.Tan, S.

(2016) J.Mol.Biol. 428: 1531-1543

  • DOI: 10.1016/j.jmb.2016.02.025

  • PubMed Abstract: 
  • Set8 is the only mammalian monomethyltransferase responsible for H4K20me1, a methyl mark critical for genomic integrity of eukaryotic cells. We present here a structural model for how Set8 uses multivalent interactions to bind and methylate the nucle ...

    Set8 is the only mammalian monomethyltransferase responsible for H4K20me1, a methyl mark critical for genomic integrity of eukaryotic cells. We present here a structural model for how Set8 uses multivalent interactions to bind and methylate the nucleosome based on crystallographic and solution studies of the Set8/nucleosome complex. Our studies indicate that Set8 employs its i-SET and c-SET domains to engage nucleosomal DNA 1 to 1.5 turns from the nucleosomal dyad and in doing so, it positions the SET domain for catalysis with H4 Lys20. Surprisingly, we find that a basic N-terminal extension to the SET domain plays an even more prominent role in nucleosome binding, possibly by making an arginine anchor interaction with the nucleosome H2A/H2B acidic patch. We further show that proliferating cell nuclear antigen and the nucleosome compete for binding to Set8 through this basic extension, suggesting a mechanism for how nucleosome binding protects Set8 from proliferating cell nuclear antigen-dependent degradation during the cell cycle.


    Organizational Affiliation

    Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
A
135Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B
102Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H2A
G
129Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
H
122Xenopus laevisMutation(s): 0 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide exchange factor SRM1
K
483Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SRM1 (MTR1, PRP20)
Find proteins for P21827 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21827
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
N-lysine methyltransferase SETD8
M
202Homo sapiensMutation(s): 0 
Gene Names: KMT5A (PRSET7, SET07, SET8, SETD8)
EC: 2.1.1.-
Find proteins for Q9NQR1 (Homo sapiens)
Go to Gene View: KMT5A
Go to UniProtKB:  Q9NQR1
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (149-MER)I149synthetic construct
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (149-MER)J149synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.397 
  • R-Value Work: 0.339 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 100.729α = 90.00
b = 300.752β = 90.00
c = 182.090γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM088236
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM111651
Damon Runyon Cancer Research FoundationUnited StatesDRG 2107-12

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-04-27
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence
  • Version 1.4: 2017-11-01
    Type: Author supporting evidence