Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3

Experimental Data Snapshot

  • Resolution: 2.85 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

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Structural basis for histone H3K4me3 recognition by the N-terminal domain of the PHD finger protein Spp1.

He, C.Liu, N.Xie, D.Liu, Y.Xiao, Y.Li, F.

(2019) Biochem J 476: 1957-1973

  • DOI: https://doi.org/10.1042/BCJ20190091
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Saccharomyces cerevisiae Spp1, a plant homeodomain (PHD) finger containing protein, is a critical subunit of the histone H3K4 methyltransferase complex of proteins associated with Set1 (COMPASS). The chromatin binding affinity of the PHD finger of Spp1 has been proposed to modulate COMPASS activity. During meiosis, Spp1 plays another role in promoting programmed double-strand break (DSB) formation by binding H3K4me3 via its PHD finger and interacting with a DSB protein, Mer2. However, how the Spp1 PHD finger performs site-specific readout of H3K4me3 is still not fully understood. In the present study, we determined the crystal structure of the highly conserved Spp1 N-terminal domain (Sc_Spp1 NTD ) in complex with the H3K4me3 peptide. The structure shows that Sc_Spp1 NTD comprises a PHD finger responsible for methylated H3K4 recognition and a C3H-type zinc finger necessary to ensure the overall structural stability. Our isothermal titration calorimetry results show that binding of H3K4me3 to Sc_Spp1 NTD is mildly inhibited by H3R2 methylation, weakened by H3T6 phosphorylation, and abrogated by H3T3 phosphorylation. This histone modification cross-talk, which is conserved in the Saccharomyces pombe and mammalian orthologs of Sc_Spp1 in vitro , can be rationalized structurally and might contribute to the roles of Spp1 in COMPASS activity regulation and meiotic recombination.

  • Organizational Affiliation

    Anhui Key Laboratory of Modern Biomanufacturing and School of Life Sciences, Anhui University, Hefei, Anhui 230601, China chaohe@ahu.edu.cn lifudong@ustc.edu.cn.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COMPASS component SPP1
A, B, C, D
123Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPP1
Find proteins for Q03012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03012 
Go to UniProtKB:  Q03012
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03012
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3
E, F, G, H
7Saccharomyces cerevisiae S288CMutation(s): 0 
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P61830 
Go to UniProtKB:  P61830
Entity Groups  
UniProt GroupP61830
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth B]
M [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth D],
S [auth D],
T [auth D]
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on M3L
E, F, G, H
Experimental Data & Validation

Experimental Data

  • Resolution: 2.85 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.81α = 90
b = 106.17β = 90
c = 139.83γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2019-09-11 
  • Deposition Author(s): He, C., Li, F.

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release