5DAH

Crystal structure of PZP domain of human AF10 protein fused with Histone H3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.611 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The PZP Domain of AF10 Senses Unmodified H3K27 to Regulate DOT1L-Mediated Methylation of H3K79.

Chen, S.Yang, Z.Wilkinson, A.W.Deshpande, A.J.Sidoli, S.Krajewski, K.Strahl, B.D.Garcia, B.A.Armstrong, S.A.Patel, D.J.Gozani, O.

(2015) Mol.Cell 60: 319-327

  • DOI: 10.1016/j.molcel.2015.08.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • AF10, a DOT1L cofactor, is required for H3K79 methylation and cooperates with DOT1L in leukemogenesis. However, the molecular mechanism by which AF10 regulates DOT1L-mediated H3K79 methylation is not clear. Here we report that AF10 contains a "reader ...

    AF10, a DOT1L cofactor, is required for H3K79 methylation and cooperates with DOT1L in leukemogenesis. However, the molecular mechanism by which AF10 regulates DOT1L-mediated H3K79 methylation is not clear. Here we report that AF10 contains a "reader" domain that couples unmodified H3K27 recognition to H3K79 methylation. An AF10 region consisting of a PHD finger-Zn knuckle-PHD finger (PZP) folds into a single module that recognizes amino acids 22-27 of H3, and this interaction is abrogated by H3K27 modification. Structural studies reveal that H3 binding triggers rearrangement of the PZP module to form an H3(22-27)-accommodating channel and that the unmodified H3K27 side chain is encased in a compact hydrogen-bond acceptor-lined cage. In cells, PZP recognition of H3 is required for H3K79 dimethylation, expression of DOT1L-target genes, and proliferation of DOT1L-addicted leukemic cells. Together, our results uncover a pivotal role for H3K27-via readout by the AF10 PZP domain-in regulating the cancer-associated enzyme DOT1L.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.,Pediatrics and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA. Electronic address: ogozani@stanford.edu.,Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Electronic address: pateld@mskcc.org.,Epigenetics Program and Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA.,Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein AF-10
A, B
208Homo sapiensMutation(s): 0 
Gene Names: MLLT10 (AF10)
Find proteins for P55197 (Homo sapiens)
Go to Gene View: MLLT10
Go to UniProtKB:  P55197
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3 peptide
C, D
11Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 2 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.611 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.905α = 90.00
b = 79.995β = 102.01
c = 59.287γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-08-19 
  • Released Date: 2015-10-21 
  • Deposition Author(s): Chen, S., Patel, D.J.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41 GM103403

Revision History 

  • Version 1.0: 2015-10-21
    Type: Initial release
  • Version 1.1: 2015-11-11
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations