Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.72 kDa 
• Atom Count: 1237 
• Residue Count: 143 
• Unique protein chains: 2

3DB3

Crystal structure of the tandem tudor domains of the E3 ubiquitin-protein ligase UHRF1 in complex with trimethylated histone H3-K9 peptide

• DOI: 10.2210/pdb3DB3/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-30 Released: 2008-09-16 
• Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Dong, A., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.282 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Literature

Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein.

Nady, N., Lemak, A., Walker, J.R., Avvakumov, G.V., Kareta, M.S., Achour, M., Xue, S., Duan, S., Allali-Hassani, A., Zuo, X., Wang, Y.X., Bronner, C., Chedin, F., Arrowsmith, C.H., Dhe-Paganon, S.

(2011) J Biol Chem 286: 24300-24311

• PubMed: 21489993 
• DOI: 10.1074/jbc.M111.234104
• Primary Citation of Related Structures:  
  3DB3, 3DB4, 2L3R


• PubMed Abstract: 
  

Histone modifications and DNA methylation represent two layers of heritable epigenetic information that regulate eukaryotic chromatin structure and gene activity. UHRF1 is a unique factor that bridges these two layers; it is required for maintenance DNA methylation at hemimethylated CpG sites, which are specifically recognized through its SRA domain and also interacts with histone H3 trimethylated on lysine 9 (H3K9me3) in an unspecified manner. Here we show that UHRF1 contains a tandem Tudor domain (TTD) that recognizes H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3). Solution NMR and crystallographic data reveal the TTD simultaneously recognizes H3K9me3 through a conserved aromatic cage in the first Tudor subdomain and unmodified H3K4 within a groove between the tandem subdomains. The subdomains undergo a conformational adjustment upon peptide binding, distinct from previously reported mechanisms for dual histone mark recognition. Mutant UHRF1 protein deficient for H3K4me0/K9me3 binding shows altered localization to heterochromatic chromocenters and fails to reduce expression of a target gene, p16(INK4A), when overexpressed. Our results demonstrate a novel recognition mechanism for the combinatorial readout of histone modification states associated with gene silencing and add to the growing evidence for coordination of, and cross-talk between, the modification states of H3K4 and H3K9 in regulation of gene expression.

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Organizational Affiliation: 

Ontario Cancer Institute, and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A	161	Homo sapiens	Mutation(s): 0  Gene Names: UHRF1, ICBP90, NP95, RNF106 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q96T88 (Homo sapiens) Explore Q96T88  Go to UniProtKB:  Q96T88
NIH Common Fund Data Resources
PHAROS  Q96T88 GTEx  ENSG00000276043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Trimethylated histone H3-K9 peptide	B	6	N/A	Mutation(s): 0
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3  Go to UniProtKB:  Q71DI3
NIH Common Fund Data Resources
PHAROS  Q71DI3 GTEx  ENSG00000183598GTEx  ENSG00000203811GTEx  ENSG00000203852

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
M3L	B	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.282 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.622	α = 90
b = 99.622	β = 90
c = 41.232	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-05-30 
• Released Date: 2008-09-16 
Deposition Author(s): Walker, J.R., Avvakumov, G.V., Xue, S., Dong, A., Li, Y., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History 

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-04-18
  Changes: Database references