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: 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence 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 (PDB Primary Data), 2.1.1.354 (UniProt)
UniProt
Find proteins for A6ZT27 (Saccharomyces cerevisiae (strain YJM789))
Explore A6ZT27 
Go to UniProtKB:  A6ZT27
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence 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))
Explore P43132 
Go to UniProtKB:  P43132
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COMPASS component SDC1C [auth M], D [auth N]42Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SDC1CPS25SAF19YDR469W
UniProt
Find proteins for Q03323 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03323 
Go to UniProtKB:  Q03323
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
COMPASS component SPP1E [auth F]237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPP1CPS40SAF41YPL138C
UniProt
Find proteins for Q03012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03012 
Go to UniProtKB:  Q03012
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
COMPASS component SWD1F [auth B]412Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWD1CPS50SAF49YAR003WFUN16
UniProt
Find proteins for P39706 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39706 
Go to UniProtKB:  P39706
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
COMPASS component SWD3G [auth A]314Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWD3CPS30SAF35YBR175WYBR1237
UniProt
Find proteins for P38123 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38123 
Go to UniProtKB:  P38123
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

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