Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 9.35 kDa 
• Atom Count: 579 
• Modelled Residue Count: 59 
• Deposited Residue Count: 75 
• Unique protein chains: 2

6AT0

Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone H3 peptide containing trimethyl lysine

• PDB DOI: 10.2210/pdb6AT0/pdb

• Classification: TRANSCRIPTION
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-08-27 Released: 2017-12-06 
• Deposition Author(s): Brustad, E.M., Baril, S.A., Waters, M.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.260 
• R-Value Work: 0.241 
• R-Value Observed: 0.242 

Literature

Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis.

Baril, S.A., Koenig, A.L., Krone, M.W., Albanese, K.I., He, C.Q., Lee, G.Y., Houk, K.N., Waters, M.L., Brustad, E.M.

(2017) J Am Chem Soc 139: 17253-17256

• PubMed: 29111699 
• DOI: 10.1021/jacs.7b09223
• Primary Citation of Related Structures:  
  6ASZ, 6AT0


• PubMed Abstract: 
  

Trimethyllysine (Kme3) reader proteins are targets for inhibition due to their role in mediating gene expression. Although all such reader proteins bind Kme3 in an aromatic cage, the driving force for binding may differ; some readers exhibit evidence for cation-π interactions whereas others do not. We report a general unnatural amino acid mutagenesis approach to quantify the contribution of individual tyrosines to cation binding using the HP1 chromodomain as a model system. We demonstrate that two tyrosines (Y24 and Y48) bind to a Kme3-histone tail peptide via cation-π interactions, but linear free energy trends suggest they do not contribute equally to binding. X-ray structures and computational analysis suggest that the distance and degree of contact between Tyr residues and Kme3 plays an important role in tuning cation-π-mediated Kme3 recognition. Although cation-π interactions have been studied in a number of proteins, this work is the first to utilize direct binding assays, X-ray crystallography, and modeling, to pinpoint factors that influence the magnitude of the individual cation-π interactions.

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Organizational Affiliation: 

Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterochromatin protein 1	A	69	Drosophila melanogaster	Mutation(s): 2  Gene Names: Su(var)205, HP1, CG8409
UniProt
Find proteins for P05205 (Drosophila melanogaster) Explore P05205  Go to UniProtKB:  P05205

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
trimethyl lysine histone H3 tail peptide	B [auth P]	6	Drosophila melanogaster	Mutation(s): 0  Gene Names:  His3, His3:CG31613, CG31613, His3:CG33803, CG33803, His3:CG33806, CG33806, His3:CG33809, CG33809, His3:CG33812, CG33812, His3:CG33815, CG33815, His3:CG33818, CG33818, His3:CG33821, CG33821, His3:CG33824, CG33824, His3:CG33827, CG33827, His3:CG33830, CG33830, His3:CG33833, CG33833, His3:CG33836, CG33836, His3:CG33839, CG33839, His3:CG33842, CG33842, His3:CG33845, CG33845, His3:CG33848, CG33848, His3:CG33851, CG33851, His3:CG33854, CG33854, His3:CG33857, CG33857, His3:CG33860, CG33860, His3:CG33863, CG33863, His3:CG33866, CG33866
UniProt
Find proteins for P02299 (Drosophila melanogaster) Explore P02299  Go to UniProtKB:  P02299

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PPN	A	L-PEPTIDE LINKING	C9 H10 N2 O4		PHE
M3L	B [auth P]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.260 
• R-Value Work: 0.241 
• R-Value Observed: 0.242 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.417	α = 90
b = 76.857	β = 90
c = 76.479	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-08-27 
• Released Date: 2017-12-06 
Deposition Author(s): Brustad, E.M., Baril, S.A., Waters, M.L.

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Database references