6J2P

Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1042/BCJ20190091

  • PubMed Abstract: 
  • <i>Saccharomyces cerevisiae </i> 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 fin ...

    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

    Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China chaohe@ahu.edu.cn lifudong@ustc.edu.cn.,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.,Anhui Key Laboratory of Modern Biomanufacturing and School of Life Sciences, Anhui University, Hefei, Anhui 230601, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COMPASS component SPP1
A, B, C, D
123Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SPP1 (CPS40, SAF41)
Find proteins for Q03012 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SPP1
Go to UniProtKB:  Q03012
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3
E, F, G, H
7Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HHT1, HHT2 (SIN2)
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P61830
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
E, F, G, H
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.234 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.810α = 90.00
b = 106.170β = 90.00
c = 139.830γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHENIXphasing
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-01-02 
  • Released Date: 2019-09-11 
  • Deposition Author(s): He, C., Li, F.

Revision History 

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