4L7X

Crystal structure of the DIDO PHD finger in complex with H3K4me3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.132 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Dido3 PHD Modulates Cell Differentiation and Division.

Gatchalian, J.Futterer, A.Rothbart, S.B.Tong, Q.Rincon-Arano, H.Sanchez de Diego, A.Groudine, M.Strahl, B.D.Martinez-A, C.van Wely, K.H.Kutateladze, T.G.

(2013) Cell Rep 4: 148-158

  • DOI: 10.1016/j.celrep.2013.06.014

  • PubMed Abstract: 
  • Death Inducer Obliterator 3 (Dido3) is implicated in the maintenance of stem cell genomic stability and tumorigenesis. Here, we show that Dido3 regulates the expression of stemness genes in embryonic stem cells through its plant homeodomain (PHD) fin ...

    Death Inducer Obliterator 3 (Dido3) is implicated in the maintenance of stem cell genomic stability and tumorigenesis. Here, we show that Dido3 regulates the expression of stemness genes in embryonic stem cells through its plant homeodomain (PHD) finger. Binding of Dido3 PHD to histone H3K4me3 is disrupted by threonine phosphorylation that triggers Dido3 translocation from chromatin to the mitotic spindle. The crystal structure of Dido3 PHD in complex with H3K4me3 reveals an atypical aromatic-cage-like binding site that contains a histidine residue. Biochemical, structural, and mutational analyses of the binding mechanism identified the determinants of specificity and affinity and explained the inability of homologous PHF3 to bind H3K4me3. Together, our findings reveal a link between the transcriptional control in embryonic development and regulation of cell division.


    Organizational Affiliation

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Death-inducer obliterator 1
A
63Homo sapiensMutation(s): 0 
Gene Names: DIDO1 (C20orf158, DATF1, KIAA0333)
Find proteins for Q9BTC0 (Homo sapiens)
Go to Gene View: DIDO1
Go to UniProtKB:  Q9BTC0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3 peptide
U
12Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
U
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.142 
  • R-Value Work: 0.132 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 40.820α = 90.00
b = 40.820β = 90.00
c = 80.620γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-24
    Type: Initial release