3FDE | pdb_00003fde

Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3FDE/pdb
• NAKB: 3FDE

• Classification: LIGASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-25 Released: 2009-01-06 
• Deposition Author(s): Hashimoto, H., Horton, J.R., Zhang, X., Cheng, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.

Hashimoto, H., Horton, J.R., Zhang, X., Cheng, X.

(2009) Epigenetics 4: 8-14

• PubMed: 19077538 
• DOI: https://doi.org/10.4161/epi.4.1.7370
• Primary Citation Related Structures: 
  3F8I, 3F8J, 3FDE


• PubMed Abstract: 
  

  Cytosine methylation in DNA is a major epigenetic signal, and plays a central role in propagating chromatin status during cell division. However the mechanistic links between DNA methylation and histone methylation are poorly understood. A multi-domain protein UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is required for DNA CpG maintenance methylation at replication forks, and mouse UHRF1-null cells show enhanced susceptibility to DNA replication arrest and DNA damaging agents. Recent data demonstrated that the SET and RING associated (SRA) domain of UHRF1 binds hemimethylated CpG and flips 5-methylcytosine out of the DNA helix, whereas its tandom tudor domain and PHD domain bind the tail of histone H3 in a highly methylation sensitive manner. We hypothesize that UHRF1 brings the two components (histones and DNA) carrying appropriate markers (on the tails of H3 and hemimethylated CpG sites) ready to be assembled into a nucleosome after replication.

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Organizational Affiliation: 
• Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.97 kDa 
• Atom Count: 5,159 
• Modeled Residue Count: 464 
• Deposited Residue Count: 472 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A, B	212	Mus musculus	Mutation(s): 0  Gene Names: Np95, Uhrf1 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8VDF2 (Mus musculus) Explore Q8VDF2  Go to UniProtKB:  Q8VDF2
IMPC:  MGI:1338889

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'	C [auth D], E [auth C]	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'	D [auth E], F	12	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	BA [auth D], CA [auth E], DA [auth E], FA [auth C], G [auth A], H [auth A], I [auth A], J [auth A], JA [auth F], K [auth A], KA [auth F], L [auth A], LA [auth F], M [auth A], MA [auth F], N [auth A], NA [auth F], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	EA [auth E], O [auth A], OA [auth F], W [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
UNL	AA [auth B], GA [auth C], HA [auth C], IA [auth C], P [auth A], Q [auth A], X [auth B], Y [auth B], Z [auth B]	Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.678	α = 90
b = 103.691	β = 90
c = 149.838	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-06 
Deposition Author(s): Hashimoto, H., Horton, J.R., Zhang, X., Cheng, X.

Revision History  

• Version 1.0: 2009-01-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-12-27
  Changes: Advisory, Data collection, Database references, Derived calculations