6BX3

Structure of histone H3k4 methyltransferase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and Conformational Dynamics of a COMPASS Histone H3K4 Methyltransferase Complex.

Qu, Q.Takahashi, Y.H.Yang, Y.Hu, H.Zhang, Y.Brunzelle, J.S.Couture, J.F.Shilatifard, A.Skiniotis, G.

(2018) Cell 174: 1117-1126.e12

  • DOI: https://doi.org/10.1016/j.cell.2018.07.020
  • Primary Citation of Related Structures:  
    6BX3, 6E29

  • PubMed Abstract: 

    The methylation of histone 3 lysine 4 (H3K4) is carried out by an evolutionarily conserved family of methyltransferases referred to as complex of proteins associated with Set1 (COMPASS). The activity of the catalytic SET domain (su(var)3-9, enhancer-of-zeste, and trithorax) is endowed through forming a complex with a set of core proteins that are widely shared from yeast to humans. We obtained cryo-electron microscopy (cryo-EM) maps of the yeast Set1/COMPASS core complex at overall 4.0- to 4.4-Å resolution, providing insights into its structural organization and conformational dynamics. The Cps50 C-terminal tail weaves within the complex to provide a central scaffold for assembly. The SET domain, snugly positioned at the junction of the Y-shaped complex, is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3). The mobile SET-I motif of the SET domain is engaged by Cps30, explaining its key role in COMPASS catalytic activity toward higher H3K4 methylation states.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: yiorgo@stanford.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-4 specificA [auth E]278Saccharomyces cerevisiae YJM789Mutation(s): 0 
Gene Names: SET1SCY_2511
EC: 2.1.1.43
UniProt
Find proteins for A6ZT27 (Saccharomyces cerevisiae (strain YJM789))
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UniProt GroupA6ZT27
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COMPASS component BRE2B [auth K]417Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRE2CPS60YLR015W
UniProt
Find proteins for P43132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COMPASS component SDC1C [auth M],
D [auth N]
42Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SDC1CPS25SAF19YDR469W
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
COMPASS component SPP1E [auth F]237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPP1CPS40SAF41YPL138C
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
COMPASS component SWD1F [auth B]412Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWD1CPS50SAF49YAR003WFUN16
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
COMPASS component SWD3G [auth A]314Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWD3CPS30SAF35YBR175WYBR1237
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIXdev-2880

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesDK090165

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence