4HP3

Crystal structure of Tet3 in complex with a CpG dsDNA

• PDB DOI:  https://doi.org/10.2210/pdb4HP3/pdb
• NAKB: 4HP3

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Xenopus tropicalis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-10-23 Released: 2012-12-05 
• Deposition Author(s): Chao, X., Tempel, W., Bian, C., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.243 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Literature

Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development.

Xu, Y., Xu, C., Kato, A., Tempel, W., Abreu, J.G., Bian, C., Hu, Y., Hu, D., Zhao, B., Cerovina, T., Diao, J., Wu, F., He, H.H., Cui, Q., Clark, E., Ma, C., Barbara, A., Veenstra, G.J., Xu, G., Kaiser, U.B., Liu, X.S., Sugrue, S.P., He, X., Min, J., Kato, Y., Shi, Y.G.

(2012) Cell 151: 1200-1213

• PubMed: 23217707 
• DOI: https://doi.org/10.1016/j.cell.2012.11.014
• Primary Citation of Related Structures:  
  4HP1, 4HP3


• PubMed Abstract: 
  

Ten-Eleven Translocation (Tet) family of dioxygenases dynamically regulates DNA methylation and has been implicated in cell lineage differentiation and oncogenesis. Yet their functions and mechanisms of action in gene regulation and embryonic development are largely unknown. Here, we report that Xenopus Tet3 plays an essential role in early eye and neural development by directly regulating a set of key developmental genes. Tet3 is an active 5mC hydroxylase regulating the 5mC/5hmC status at target gene promoters. Biochemical and structural studies further demonstrate that the Tet3 CXXC domain is critical for specific Tet3 targeting. Finally, we show that the enzymatic activity and CXXC domain are both crucial for Tet3's biological function. Together, these findings define Tet3 as a transcription regulator and reveal a molecular mechanism by which the 5mC hydroxylase and DNA binding activities of Tet3 cooperate to control target gene expression and embryonic development.

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Organizational Affiliation: 

Division of Endocrinology, Diabetes and Hypertension, Departments of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.89 kDa 
• Atom Count: 898 
• Modelled Residue Count: 75 
• Deposited Residue Count: 96 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LOC100036628 protein	C	72	Xenopus tropicalis	Mutation(s): 0  Gene Names: tet3 EC: 1.14.11
UniProt
Find proteins for A0JP82 (Xenopus tropicalis) Explore A0JP82  Go to UniProtKB:  A0JP82

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*AP*AP*CP*GP*TP*TP*GP*GP*C)-3')	A, B	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth C], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	D [auth A], E [auth A], H [auth C]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.243 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/m34hp3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.892	α = 90
b = 39.455	β = 99.92
c = 54.134	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Chao, X., Tempel, W., Bian, C., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2012-12-19
  Changes: Database references