7EBK

Mouse Trim66 PHD-Bromo dual domain complexed with the H3(1-24)K9me3K18ac peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A TRIM66/DAX1/Dux axis suppresses the totipotent 2-cell-like state in murine embryonic stem cells.

Zuo, F.Jiang, J.Fu, H.Yan, K.Liefke, R.Zhang, J.Hong, Y.Chang, Z.Liu, N.Wang, Z.Xi, Q.

(2022) Cell Stem Cell 29: 948-961.e6

  • DOI: https://doi.org/10.1016/j.stem.2022.05.004
  • Primary Citation of Related Structures:  
    7EBJ, 7EBK

  • PubMed Abstract: 

    2-cell-like cells (2CLCs)-which comprise only ∼1% of murine embryonic stem cells (mESCs)-resemble blastomeres of 2-cell-stage embryos and are used to investigate zygotic genome activation (ZGA). Here, we discovered that TRIM66 and DAX1 function together as negative regulators of the 2C-like state in mESCs. Chimeric assays confirmed that mESCs lacking TRIM66 or DAX1 function have bidirectional embryonic and extraembryonic differentiation potential. TRIM66 functions by recruiting the co-repressor DAX1 to the Dux promoter, and TRIM66's repressive effect on Dux is dependent on DAX1. A solved crystal structural shows that TRIM66's PHD finger recognizes H3K4-K9me3, and mutational evidence confirmed that TRIM66's PHD finger is essential for its repression of Dux. Thus, beyond expanding the scope of known 2CLC regulators, our study demonstrates that interventions disrupting TRIM66 or DAX1 function in mESCs yield 2CLCs with expanded bidirectional differentiation potential, opening doors for the practical application of these totipotent-like cells.


  • Organizational Affiliation

    Joint Graduate Program of Peking-Tsinghua-NIBS, Tsinghua University, Beijing 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tripartite motif-containing protein 66187Mus musculusMutation(s): 0 
Gene Names: Trim66
UniProt & NIH Common Fund Data Resources
Find proteins for Q924W6 (Mus musculus)
Explore Q924W6 
Go to UniProtKB:  Q924W6
IMPC:  MGI:2152406
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ924W6
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H3K9me3K18ac24Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68431
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.646α = 90
b = 64.646β = 90
c = 251.744γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32071204

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-10-05
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description