3SOU

Structure of UHRF1 PHD finger in complex with histone H3 1-9 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8001 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

PHD Finger Recognition of Unmodified Histone H3R2 Links UHRF1 to Regulation of Euchromatic Gene Expression.

Rajakumara, E.Wang, Z.Ma, H.Hu, L.Chen, H.Lin, Y.Guo, R.Wu, F.Li, H.Lan, F.Shi, Y.G.Xu, Y.Patel, D.J.Shi, Y.

(2011) Mol.Cell 43: 275-284

  • DOI: 10.1016/j.molcel.2011.07.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Histone methylation occurs on both lysine and arginine residues, and its dynamic regulation plays a critical role in chromatin biology. Here we identify the UHRF1 PHD finger (PHD(UHRF1)), an important regulator of DNA CpG methylation, as a histone H3 ...

    Histone methylation occurs on both lysine and arginine residues, and its dynamic regulation plays a critical role in chromatin biology. Here we identify the UHRF1 PHD finger (PHD(UHRF1)), an important regulator of DNA CpG methylation, as a histone H3 unmodified arginine 2 (H3R2) recognition modality. This conclusion is based on binding studies and cocrystal structures of PHD(UHRF1) bound to histone H3 peptides, where the guanidinium group of unmodified R2 forms an extensive intermolecular hydrogen bond network, with methylation of H3R2, but not H3K4 or H3K9, disrupting complex formation. We have identified direct target genes of UHRF1 from microarray and ChIP studies. Importantly, we show that UHRF1's ability to repress its direct target gene expression is dependent on PHD(UHRF1) binding to unmodified H3R2, thereby demonstrating the functional importance of this recognition event and supporting the potential for crosstalk between histone arginine methylation and UHRF1 function.


    Organizational Affiliation

    State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.,Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.,Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Constellation Pharmaceuticals, Cambridge, MA 02140, USA.,Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Division of Newborn Medicine and Program in Epigenetics, Department of Medicine, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Endocrinology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Biochemistry, Fudan University Medical School, Shanghai 200032, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase UHRF1
A, B
70Homo sapiensMutation(s): 0 
Gene Names: UHRF1 (ICBP90, NP95, RNF106)
EC: 2.3.2.27
Find proteins for Q96T88 (Homo sapiens)
Go to Gene View: UHRF1
Go to UniProtKB:  Q96T88
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3
D, E
9Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8001 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.215 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 43.218α = 90.00
b = 43.218β = 90.00
c = 184.347γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description