5DAH

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

• PDB DOI:  https://doi.org/10.2210/pdb5DAH/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-19 Released: 2015-10-21 
• Deposition Author(s): Chen, S., Patel, D.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.240 
• R-Value Work: 0.176 
• R-Value Observed: 0.182 

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

• PubMed: 26439302 
• DOI: https://doi.org/10.1016/j.molcel.2015.08.019
• Primary Citation of Related Structures:  
  5DAG, 5DAH


• 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" 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.

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Organizational Affiliation: 

Department of Biology, Stanford University, Stanford, CA 94305, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 49.28 kDa 
• Atom Count: 2,895 
• Modelled Residue Count: 378 
• Deposited Residue Count: 438 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein AF-10	A, B	208	Homo sapiens	Mutation(s): 0  Gene Names: MLLT10, AF10
UniProt & NIH Common Fund Data Resources
Find proteins for P55197 (Homo sapiens) Explore P55197  Go to UniProtKB:  P55197
PHAROS:  P55197

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3 peptide	C, D	11	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	J [auth A], K [auth A], Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.240 
• R-Value Work: 0.176 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.905	α = 90
b = 79.995	β = 102.01
c = 59.287	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41 GM103403

Revision History  

• Version 1.0: 2015-10-21
  Type: Initial release
  
• Version 1.1: 2015-11-11
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence