ISDA

Entry Detail

PDB ID:

3U5P

Keywords:

TRANSCRIPTION

Title:

Crystal structure of the complex of TRIM33 PHD-Bromo and H3(1-28)K9me3K14acK18acK23ac histone peptide

Biological Source:

Source Organism:

Homo sapiens

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2011-10-11

Release Date:

2012-01-18

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.80 Å

R-Value Free:

0.26

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:E3 ubiquitin-protein ligase TRIM33
Chain IDs:A, C (auth: B), E (auth: C), G (auth: D), I (auth: E), K (auth: F), M (auth: G), O (auth: H)
Chain Length:207
Number of Molecules:8
Biological Source:Homo sapiens

UniProt ID:Q9UPN9 Pfam ID:PF00628, PF00439

Protein Blast

Polymer Type:polypeptide(L)
Description:Histone H3.1
Chain IDs:B (auth: I), D (auth: J), F (auth: K), H (auth: L), J (auth: M), L (auth: N), N (auth: O), P
Chain Length:28
Number of Molecules:8
Biological Source:Homo sapiens

UniProt ID:P68431

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
ALY	B	LYS	N(6)-ACETYLLYSINE
M3L	B	LYS	N-TRIMETHYLLYSINE

Ligand Molecules

Primary Citation

A poised chromatin platform for TGF-beta access to master regulators

Xi, Q, Wang, Z, Zaromytidou, A.I, Zhang, X.H, Chow-Tsang, L.F, Liu, J.X, Kim, H, Barlas, A, Manova-Todorova, K, Kaartinen, V, Studer, L, Mark, W, Patel, D.J, Massague, J.Show

Cell(Cambridge,Mass.) 147 1511 1524 (2011)

PMID: 22196728 DOI: 10.1016/j.cell.2011.11.032

Abstact

Specific chromatin marks keep master regulators of differentiation silent yet poised for activation by extracellular signals. We report that nodal TGF-β signals use the poised histone mark H3K9me3 to trigger differentiation of mammalian embryonic stem cells. Nodal receptors induce the formation of companion Smad4-Smad2/3 and TRIM33-Smad2/3 complexes. The PHD-Bromo cassette of TRIM33 facilitates binding of TRIM33-Smad2/3 to H3K9me3 and H3K18ac on the promoters of mesendoderm regulators Gsc and Mixl1. The crystal structure of this cassette, bound to histone H3 peptides, illustrates that PHD recognizes K9me3, and Bromo binds an adjacent K18ac. The interaction between TRIM33-Smad2/3 and H3K9me3 displaces the chromatin-compacting factor HP1γ, making nodal response elements accessible to Smad4-Smad2/3 for Pol II recruitment. In turn, Smad4 increases K18 acetylation to augment TRIM33-Smad2/3 binding. Thus, nodal effectors use the H3K9me3 mark as a platform to switch master regulators of stem cell differentiation from the poised to the active state.

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Primary Citation of related structures